Abstract
The plant pathogen, Bipolaris sorokiniana (teleomorph: Cochliobolus sativus), is of global concern as it attacks many economically important cereals and grasses. During the infection process, phytopathogenic fungi are known to secrete a variety of proteins collectively known as the secretome, analyzing which can help in deciphering the mechanism of fungal pathogenesis. In this study, we performed in silico secretome analysis of C. sativus strain ND90Pr using established secretome prediction pipeline involving software tools such as SignalP, TargetP, TMHMM, big-PI Fungal Predictor, ProtComp, and WoLF PSORT. Using these software and other prediction criteria, we identified 196 probable secretory proteins from the B. sorokiniana proteome. Characterization of the predicted secretome revealed proteins that may have probable functions in degradation of the plant cell wall, lipids, proteins, and nucleic acids, as well as in pathogenesis and metabolism. Further, the PHI-base analysis identified 38 proteins having a possible role in pathogenicity and virulence. This study helped to predict the composition of the secretome of B. sorokiniana and extrapolate its role in plant infection and pathogen survival. It may provide clues for developing new control strategies targeting the vital fungal secretory proteins.
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Data availability
The proteome of C. sativus strain ND90Pr (anamorph: B. sorokiniana) v 1.0 used in the study was downloaded from the JGI Mycocosm database (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Cocsa1). The analyzed data and the datasets supporting the conclusions of this article are included within the article and the associated Online Resources.
Abbreviations
- Aa:
-
Amino acid
- Avr:
-
Avirulence
- CHRD:
-
Chordin
- CWDEs:
-
Cell wall degrading enzymes
- ECM:
-
Extracellular matrix
- ETS:
-
Effector-triggered susceptibility
- FAD:
-
Flavin adenine dinucleotide
- GH:
-
Glycosyl hydrolase
- GMC:
-
Glucose methanol choline
- GPI:
-
Glycosylphosphatidylinositol
- LysM:
-
Lysine motif
- PHI:
-
Pathogen Host Interaction database
- pI:
-
Isoelectric point
- SCR:
-
Small and cysteine-rich
- START:
-
StAR related lipid transfer
- TM:
-
Transmembrane domain
- TMHMM:
-
Transmembrane Helices Hidden Markov Model
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Acknowledgements
The authors thank Ms. Pooja Sethiya (CSIR-NCL, Pune, India) and Ms. Meenakshi Kapase (CSIR-NCL, Pune, India) for initial technical support. GMP acknowledges the Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India for the Ph.D. research program, and thanks the Department of Science and Technology (DST), India for the INSPIRE research fellowship.
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NYK acknowledges the Council of Scientific and Industrial Research (CSIR; https://www.csir.res.in/), India (grant number: BSC 0117), and the Department of Biotechnology (DBT; http://www.dbtindia.gov.in/), India (grant number: GAP 319026) for financial support. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.
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Conceptualization: Gauri M. Pathak and Narendra Y. Kadoo; Methodology: Gauri M. Pathak and Gayatri S. Gurjar; Formal analysis and investigation: Gauri M. Pathak; Writing - original draft preparation: Gauri M. Pathak; Writing - review and editing: Gauri M. Pathak, Gayatri S. Gurjar and Narendra Y. Kadoo; Funding acquisition: Narendra Y. Kadoo; Resources: Narendra Y. Kadoo; Supervision: Narendra Y. Kadoo.
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Pathak, G.M., Gurjar, G.S. & Kadoo, N.Y. Insights of Bipolaris sorokiniana secretome - an in silico approach. Biologia 75, 2367–2381 (2020). https://doi.org/10.2478/s11756-020-00537-4
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DOI: https://doi.org/10.2478/s11756-020-00537-4