In silico characterization of differentially expressed short-read nucleotide sequences identified in dieback stress-induced transcriptomic analysis reveals their role as antimicrobial peptides

Frontiers in Plant Science

Plant Science

Ghalia Nadeem¹  Siddra Ijaz¹  Riffat Malik¹  Hayssam M. Ali²  Imran Ul Haq³  Sukhwinder Kaur⁴ 

[1]Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan

[2]Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia

[3]Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan

[4]Department of Plant Pathology, University of California, Davis, Davis, CA, United States

关键词: antimicrobial peptides;    resistance genes;    RGAs;    homology modelling;    fingerprints;   

DOI  :  10.3389/fpls.2023.1168221

 received in 2023-02-17, accepted in 2023-03-02,  发布年份 2023

来源: Frontiers

【 摘 要 】

We investigated the in silico characterization of short-length nucleotide sequences that were differentially expressed in dieback stress-induced transcriptomic analysis. They displayed homology with C-terminal flanking peptides and defensins-like proteins, revealing their antimicrobial activity. Their predicted fingerprints displayed protein signatures related to antimicrobial peptides. These short-length RGAs have been shown to possess structural motifs such as APLT P-type ATPase, casein kinase II (CK2), protein kinase 3, protein kinase C (PKC), and N-glycosylation site that are the attributes of disease resistance genes. The prediction of arginine and lysine residues in active binding sites in ligand docking analysis prophesied them as antimicrobial peptides due to their strong relation with antimicrobial activity. The in silico structural–functional characterization has predicted their role in resistance against microbial pathogens. Moreover, the predicted antimicrobial peptide regions showed their homology with the signature domain of PR-5-like protein and AMP family Thaumatin

【 授权许可】

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Copyright © 2023 Ijaz, Haq, Malik, Nadeem, Ali and Kaur