Bioinformatics-Coupled Molecular Approaches for Unravelling Potential Antimicrobial Peptides Coding Genes in Brazilian Native and Crop Plant Species

Abstract

As eukaryotes, plants include in innate defense antimicrobial peptides (AMP), usually small cysteine or glycine-rich peptides effective against a wide range of pathogens. The main classes of AMPs are represented by alpha/beta-defensins, lipid-transfer proteins, thionins, cyclotides, snakins and hevein-like, according to amino acid sequence homology. In spite of increasing number of described AMPs from plants, last decade advances in methodologies for gene expression and the huge amounts of genomic, proteomic and other "-omics" data lead to new prospection strategies of novel potential candidates. Organised user-friendly databases are available to be searched and enlarged with newly discovered plant-derived AMPs. Bioinformatics has allowed the application of in silico-associated molecular tools aiming to screen and identify genes coding for these peptides, starting from genome, transcriptomes, proteome or metabolome from various cultivated or wild plants. As expected, crop plants have been the main target for AMP research and application, also because the higher availability of molecular data. However, wild plant species biodiversity and results for AMP search have increased the importance of characterization in native plants. Enormous plant diversity in Brazilian ecosystems summed to croplands provides potential targets to identify novel candidates for plant AMP. Despite these opportunities, bioinformatics tools are restricted to species whose "-omics" are available, otherwise only heterology-based analyses are feasible, as it has been the case of most Brazilian plant AMP prospection research groups. Still rare, but promising results indicate that this research field on Brazilian crop/native species presents a growing trend of application in agriculture, medicine and industry.

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

“…In genomics, DNA sequencing and mapping constitute a high yield and an useful step for seeking AMPcoding genes (Pestana-Calsa et al 2010;Pestana-Calsa and Calsa Jr. 2011). One of the most used methods for AMP discovery is the analysis of homologs of known genes by comparing new sequences with sequences of biochemically characterized AMPs Pestana-Calsa and Calsa Jr. 2011), since the sequence segments with high identity tend to share structure and function.…”

“…Peptidomics addresses the study of small polypeptides, eg by coupling bi-or multidimensional liquid chromatography to mass spectrometry (Pestana-Calsa et al 2010). Thirty-four novel AMPs from skin secretions of Rana nigrovittata were identified by integrating genomics and peptidomics analysis .…”

Prediction of Antimicrobial Peptides Based on Sequence Alignment and Feature Selection Methods

“…Thus, AMPs have attracted the attention of many investigators as a substitute for conventional antibiotics [1]. Currently, most researchers in this area are focused on screening and in silico modeling novel AMPs [6], [7] as computational approaches can accelerate the process of antimicrobial drug discovery and design [8]. Many bioinformatics methods have been developed for predicting new AMPs.…”

Species specific approach to the development of web-based antimicrobial peptides prediction tool for cattle

“…These AMP molecules can be further classified as cationic or anionic depending on net charge on them. AMPs comprise of classes like defensins, thionins, lipidtransfer proteins, cyclotides, snakins and hevein-like, according to amino acid sequence homology (Pestana-Calsa et al, 2010). Some of the bovine AMPs with commercial use like Lactoferricin, Lactoferrampin, Alpha and Beta lactoglobulin derived peptides, casein derived peptides, lysozyme derived peptide (Jabbari et al, 2012) are well documented.…”