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Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens.

Williams HL, Sturrock RN, Islam MA, Hammett C, Ekramoddoullah AK, Leal I - BMC Genomics (2014)

Bottom Line: Many of these putative virulence factors were also among 82 genes identified as encoding putatively secreted proteins.Significantly down-regulated genes included a manganese-superoxide dismutase, two metalloproteases, and an unknown putatively secreted protein called Ps0058.This first collection of Phellinus sulphurascens EST sequences and its annotation provide an important resource for future research aimed at understanding key virulence factors of this forest pathogen.

View Article: PubMed Central - PubMed

Affiliation: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria V8Z 1M5, BC, Canada. Holly.Williams@NRCan-RNCan.gc.ca.

ABSTRACT

Background: Phellinus sulphurascens is a fungal pathogen that causes laminar root rot in conifers, one of the most damaging root diseases in western North America. Despite its importance as a forest pathogen, this fungus is still poorly studied at the genomic level. An understanding of the molecular events involved in establishment of the disease should help to develop new methods for control of this disease.

Results: We generated over 4600 expressed sequence tags from two cDNA libraries constructed using either mycelia grown on cellophane sheets and exposed to Douglas-fir roots or tissues from P. sulphurascens-infected Douglas-fir roots. A total of 890 unique genes were identified from the two libraries, and functional classification of 636 of these genes was possible using the Functional Catalogue (FunCat) annotation scheme. cDNAs were identified that encoded 79 potential virulence factors, including numerous genes implicated in virulence in a variety of phytopathogenic fungi. Many of these putative virulence factors were also among 82 genes identified as encoding putatively secreted proteins. The expression patterns of 86 selected fungal genes over 7 days of infection of Douglas-fir were examined using real-time PCR, and those significantly up-regulated included rhamnogalacturonan acetylesterase, 1,4-benzoquinone reductase, a cyclophilin, a glucoamylase, 3 hydrophobins, a lipase, a serine carboxypeptidase, a putative Ran-binding protein, and two unknown putatively secreted proteins called 1 J04 and 2 J12. Significantly down-regulated genes included a manganese-superoxide dismutase, two metalloproteases, and an unknown putatively secreted protein called Ps0058.

Conclusions: This first collection of Phellinus sulphurascens EST sequences and its annotation provide an important resource for future research aimed at understanding key virulence factors of this forest pathogen. We examined the expression patterns of numerous fungal genes with potential roles in virulence, and found a collection of functionally diverse genes that are significantly up- or down-regulated during infection of Douglas-fir seedling roots by P. sulphurascens.

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Functional classification of 378 ESTs from theP. sulphurascens-Douglas-fir library with significant similarities to fungal genes available in GenBank. The putative genes were classified into functional categories following the Munich Information Center for Protein Sequences Functional Categories (MIPS FunCat) annotation scheme [56].
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Fig2: Functional classification of 378 ESTs from theP. sulphurascens-Douglas-fir library with significant similarities to fungal genes available in GenBank. The putative genes were classified into functional categories following the Munich Information Center for Protein Sequences Functional Categories (MIPS FunCat) annotation scheme [56].

Mentions: Of the 446 ESTs from the Ps-DF library that shared significant similarity with fungal sequences in the public databases, functional annotation was possible for 85% (83% of the unisequences). We excluded all sequences with no significant similarities to known sequences (E-value > 10−5) in our analyses of this library, because it was uncertain whether they originated from Ps or DF. Of the 380 annotated ESTs, approximately 9.7% were involved in metabolism, 10.5% in protein fate, 6.6% in transport, 11.8% in energy, 5.8% in protein synthesis, 1.8% in cell wall degradation, 4.2% in cell rescue, disease, and virulence, and 37.9% were ribosomal proteins (Figure 2). Unclassified proteins accounted for 15% of the total fungal ESTs from this library.Figure 2


Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens.

Williams HL, Sturrock RN, Islam MA, Hammett C, Ekramoddoullah AK, Leal I - BMC Genomics (2014)

Functional classification of 378 ESTs from theP. sulphurascens-Douglas-fir library with significant similarities to fungal genes available in GenBank. The putative genes were classified into functional categories following the Munich Information Center for Protein Sequences Functional Categories (MIPS FunCat) annotation scheme [56].
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4117978&req=5

Fig2: Functional classification of 378 ESTs from theP. sulphurascens-Douglas-fir library with significant similarities to fungal genes available in GenBank. The putative genes were classified into functional categories following the Munich Information Center for Protein Sequences Functional Categories (MIPS FunCat) annotation scheme [56].
Mentions: Of the 446 ESTs from the Ps-DF library that shared significant similarity with fungal sequences in the public databases, functional annotation was possible for 85% (83% of the unisequences). We excluded all sequences with no significant similarities to known sequences (E-value > 10−5) in our analyses of this library, because it was uncertain whether they originated from Ps or DF. Of the 380 annotated ESTs, approximately 9.7% were involved in metabolism, 10.5% in protein fate, 6.6% in transport, 11.8% in energy, 5.8% in protein synthesis, 1.8% in cell wall degradation, 4.2% in cell rescue, disease, and virulence, and 37.9% were ribosomal proteins (Figure 2). Unclassified proteins accounted for 15% of the total fungal ESTs from this library.Figure 2

Bottom Line: Many of these putative virulence factors were also among 82 genes identified as encoding putatively secreted proteins.Significantly down-regulated genes included a manganese-superoxide dismutase, two metalloproteases, and an unknown putatively secreted protein called Ps0058.This first collection of Phellinus sulphurascens EST sequences and its annotation provide an important resource for future research aimed at understanding key virulence factors of this forest pathogen.

View Article: PubMed Central - PubMed

Affiliation: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria V8Z 1M5, BC, Canada. Holly.Williams@NRCan-RNCan.gc.ca.

ABSTRACT

Background: Phellinus sulphurascens is a fungal pathogen that causes laminar root rot in conifers, one of the most damaging root diseases in western North America. Despite its importance as a forest pathogen, this fungus is still poorly studied at the genomic level. An understanding of the molecular events involved in establishment of the disease should help to develop new methods for control of this disease.

Results: We generated over 4600 expressed sequence tags from two cDNA libraries constructed using either mycelia grown on cellophane sheets and exposed to Douglas-fir roots or tissues from P. sulphurascens-infected Douglas-fir roots. A total of 890 unique genes were identified from the two libraries, and functional classification of 636 of these genes was possible using the Functional Catalogue (FunCat) annotation scheme. cDNAs were identified that encoded 79 potential virulence factors, including numerous genes implicated in virulence in a variety of phytopathogenic fungi. Many of these putative virulence factors were also among 82 genes identified as encoding putatively secreted proteins. The expression patterns of 86 selected fungal genes over 7 days of infection of Douglas-fir were examined using real-time PCR, and those significantly up-regulated included rhamnogalacturonan acetylesterase, 1,4-benzoquinone reductase, a cyclophilin, a glucoamylase, 3 hydrophobins, a lipase, a serine carboxypeptidase, a putative Ran-binding protein, and two unknown putatively secreted proteins called 1 J04 and 2 J12. Significantly down-regulated genes included a manganese-superoxide dismutase, two metalloproteases, and an unknown putatively secreted protein called Ps0058.

Conclusions: This first collection of Phellinus sulphurascens EST sequences and its annotation provide an important resource for future research aimed at understanding key virulence factors of this forest pathogen. We examined the expression patterns of numerous fungal genes with potential roles in virulence, and found a collection of functionally diverse genes that are significantly up- or down-regulated during infection of Douglas-fir seedling roots by P. sulphurascens.

Show MeSH
Related in: MedlinePlus