Secretome Analysis of Fusarium udum

In order to determine the secretory signal peptides, SignalP v4.1 (Nielsen, 2017 (link))⁴ was used to examine the 16,179 predicted proteins of F. udum. Further, TMHMM v2.0 was used to predict the protein sets with the existence of transmembrane domains (Krogh et al., 2001 (link)) and GPI (glycosylphosphatidyl inositol)-anchor using PredGPI (Pierleoni et al., 2008 (link)). Proteins including one transmembrane domain situated within the N-terminal signal peptide and no transmembrane domain overall were chosen. The predicted secretory proteins’ cysteine content was examined. In order to functionally annotate the predicted secretome, BLAST2GO was used to assign GO keywords (Altschul et al., 1990 (link)). The dbCAN HMMs 5.0 (Yin et al., 2012 (link)) was used to find carbohydrate metabolism active enzymes (CAZymes) based on the CAZy database in the F. udum secretome.

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Srivastava A.K., Srivastava R., Yadav J., Singh A.K., Tiwari P.K., Srivastava A.K., Sahu P.K., Singh S.M, & Kashyap P.L. (2023). Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea. Frontiers in Microbiology, 14, 1066096.

Publication 2023

Carbohydrate metabolism Cysteine Enzymes Glycosylphosphatidyl inositol Hmms Proteins Secretome Secretory Sets domains Signal peptide

Corresponding Organization : National Bureau of Agriculturally Important Microorganisms

Other organizations : Banaras Hindu University, Indian Institute of Wheat and Barley Research

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Variable analysis

independent variables

Use of SignalP v4.1 to examine the 16,179 predicted proteins of F. udum
Use of TMHMM v2.0 to predict the protein sets with the existence of transmembrane domains
Use of PredGPI to predict GPI (glycosylphosphatidyl inositol)-anchor
Selection of proteins including one transmembrane domain situated within the N-terminal signal peptide and no transmembrane domain overall
Examination of the predicted secretory proteins' cysteine content
Use of BLAST2GO to assign GO keywords to functionally annotate the predicted secretome
Use of the dbCAN HMMs 5.0 to find carbohydrate metabolism active enzymes (CAZymes) in the F. udum secretome

dependent variables

Identification of secretory signal peptides in the 16,179 predicted proteins of F. udum
Identification of proteins with transmembrane domains and GPI-anchor
Identification of proteins with one transmembrane domain situated within the N-terminal signal peptide and no transmembrane domain overall
Characterization of the cysteine content of the predicted secretory proteins
Functional annotation of the predicted secretome using GO keywords
Identification of carbohydrate metabolism active enzymes (CAZymes) in the F. udum secretome

control variables

Independent variables not explicitly mentioned.
Dependent variables not explicitly mentioned.
Positive and negative controls not specified.

Annotations

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