Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici
Abstract Background Gray leaf spot is a devastating disease caused by Stemphylium lycopersici that threatens tomato-growing areas worldwide. Typically, many pathogenesis-related and unrelated secreted proteins can be predicted in genomes using bioinformatics and computer-based prediction algorithms,...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-11-01
|
| Series: | BMC Microbiology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12866-018-1329-y |
| _version_ | 1811204650267836416 |
|---|---|
| author | Rong Zeng Shigang Gao Lihui Xu Xin Liu Fuming Dai |
| author_facet | Rong Zeng Shigang Gao Lihui Xu Xin Liu Fuming Dai |
| author_sort | Rong Zeng |
| collection | DOAJ |
| description | Abstract Background Gray leaf spot is a devastating disease caused by Stemphylium lycopersici that threatens tomato-growing areas worldwide. Typically, many pathogenesis-related and unrelated secreted proteins can be predicted in genomes using bioinformatics and computer-based prediction algorithms, which help to elucidate the molecular mechanisms of pathogen-plant interactions. Results S. lycopersici-secreted proteins were predicted from 8997 proteins using a set of internet-based programs, including SignalP v4.1 TMHMM v2.0, big-PI Fungal Predictor, ProtComp V9.0 and TargetP v1.1. Analysis showed that 511 proteins are predicted to be secreted. These proteins vary from 51 to 600 residues in length, with signal peptides ranging from 14 to 30 residues in length. Functional analysis of differentially expressed proteins was performed using Blast2GO. Gene ontology analysis of 305 proteins classified them into 8 groups in biological process (BP), 6 groups in molecular function (MF), and 10 groups in cellular component (CC). Pathogen-host interaction (PHI) partners were predicted by performing BLASTp analysis of the predicted secreted proteins against the PHI database. In total, 159 secreted proteins in S. lycopersici might be involved in pathogenicity and virulence pathways. Scanning S. lycopersici-secreted proteins for the presence of carbohydrate-active enzyme (CAZyme)-coding gene homologs resulted in the prediction of 259 proteins. In addition, 12 of the 511 proteins predicted to be secreted are small cysteine-rich proteins (SCRPs). Conclusions S. lycopersici secretory proteins have not yet been studied. The study of S. lycopersici genes predicted to encode secreted proteins is highly significant for research aimed at understanding the hypothesized roles of these proteins in host penetration, tissue necrosis, immune subversion and the identification of new targets for fungicides. |
| first_indexed | 2024-04-12T03:16:09Z |
| format | Article |
| id | doaj.art-152ba49211a645aa8eb02a1ad70354df |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-04-12T03:16:09Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-152ba49211a645aa8eb02a1ad70354df2022-12-22T03:50:04ZengBMCBMC Microbiology1471-21802018-11-0118111010.1186/s12866-018-1329-yPrediction of pathogenesis-related secreted proteins from Stemphylium lycopersiciRong Zeng0Shigang Gao1Lihui Xu2Xin Liu3Fuming Dai4Institute of Eco-Environment and Plant Protection, Shanghai Key Laboratory of Protection Horticultural Technology, Shanghai Academy of Agricultural SciencesInstitute of Eco-Environment and Plant Protection, Shanghai Key Laboratory of Protection Horticultural Technology, Shanghai Academy of Agricultural SciencesInstitute of Eco-Environment and Plant Protection, Shanghai Key Laboratory of Protection Horticultural Technology, Shanghai Academy of Agricultural SciencesInstitute of Eco-Environment and Plant Protection, Shanghai Key Laboratory of Protection Horticultural Technology, Shanghai Academy of Agricultural SciencesInstitute of Eco-Environment and Plant Protection, Shanghai Key Laboratory of Protection Horticultural Technology, Shanghai Academy of Agricultural SciencesAbstract Background Gray leaf spot is a devastating disease caused by Stemphylium lycopersici that threatens tomato-growing areas worldwide. Typically, many pathogenesis-related and unrelated secreted proteins can be predicted in genomes using bioinformatics and computer-based prediction algorithms, which help to elucidate the molecular mechanisms of pathogen-plant interactions. Results S. lycopersici-secreted proteins were predicted from 8997 proteins using a set of internet-based programs, including SignalP v4.1 TMHMM v2.0, big-PI Fungal Predictor, ProtComp V9.0 and TargetP v1.1. Analysis showed that 511 proteins are predicted to be secreted. These proteins vary from 51 to 600 residues in length, with signal peptides ranging from 14 to 30 residues in length. Functional analysis of differentially expressed proteins was performed using Blast2GO. Gene ontology analysis of 305 proteins classified them into 8 groups in biological process (BP), 6 groups in molecular function (MF), and 10 groups in cellular component (CC). Pathogen-host interaction (PHI) partners were predicted by performing BLASTp analysis of the predicted secreted proteins against the PHI database. In total, 159 secreted proteins in S. lycopersici might be involved in pathogenicity and virulence pathways. Scanning S. lycopersici-secreted proteins for the presence of carbohydrate-active enzyme (CAZyme)-coding gene homologs resulted in the prediction of 259 proteins. In addition, 12 of the 511 proteins predicted to be secreted are small cysteine-rich proteins (SCRPs). Conclusions S. lycopersici secretory proteins have not yet been studied. The study of S. lycopersici genes predicted to encode secreted proteins is highly significant for research aimed at understanding the hypothesized roles of these proteins in host penetration, tissue necrosis, immune subversion and the identification of new targets for fungicides.http://link.springer.com/article/10.1186/s12866-018-1329-yTomato leaf gray spot diseaseSignal peptideEffectorPathogen-host interactionCAZymesSCRSPs |
| spellingShingle | Rong Zeng Shigang Gao Lihui Xu Xin Liu Fuming Dai Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici BMC Microbiology Tomato leaf gray spot disease Signal peptide Effector Pathogen-host interaction CAZymes SCRSPs |
| title | Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici |
| title_full | Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici |
| title_fullStr | Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici |
| title_full_unstemmed | Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici |
| title_short | Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici |
| title_sort | prediction of pathogenesis related secreted proteins from stemphylium lycopersici |
| topic | Tomato leaf gray spot disease Signal peptide Effector Pathogen-host interaction CAZymes SCRSPs |
| url | http://link.springer.com/article/10.1186/s12866-018-1329-y |
| work_keys_str_mv | AT rongzeng predictionofpathogenesisrelatedsecretedproteinsfromstemphyliumlycopersici AT shiganggao predictionofpathogenesisrelatedsecretedproteinsfromstemphyliumlycopersici AT lihuixu predictionofpathogenesisrelatedsecretedproteinsfromstemphyliumlycopersici AT xinliu predictionofpathogenesisrelatedsecretedproteinsfromstemphyliumlycopersici AT fumingdai predictionofpathogenesisrelatedsecretedproteinsfromstemphyliumlycopersici |