High‐performance computational analysis and peptide screening from databases of cyclotides from poaceae

Abstract

Cyclotides are a family of head-to-tail cyclized peptides containing three conserved disulfide bonds, in a structural scaffold also known as a cyclic cysteine knot. Due to the high degree of cysteine conservation, novel members from this peptide family can be identified in protein databases through a search through regular expression (REGEX). In this work, six novel cyclotide-like precursors from the Poaceae were identified from NCBI's non-redundant protein database by the use of REGEX. Two out of six sequences (named Zea mays L and M) showed an Asp residue in the C-terminal, which indicated that they could be cyclic. Gene expression in maize tissues was investigated, showing that the previously described cyclotide-like Z. mays J is expressed in the roots. According to molecular dynamics, the structure of Z. mays J seems to be stable, despite the putative absence of cyclization. As regards cyclotide evolution, it was hypothesized that this is an outcome from convergent evolution and/or horizontal gene transfer. The results showed that peptide screening from databases should be performed periodically in order to include novel sequences, which are deposited as the databases grow. Indeed, the advances in computational and experimental methods will together help to answer key questions and reach new horizons in defense-related peptide identification.

Comparative transcriptomic analysis indicates genes associated with local and systemic resistance to Colletotrichum graminicola in maize

“…Cysteine patterns described by Silverstein 26 for the main AMP classes 26, 39 were used for AMP identification in the NCBI RefSeq proteins annotated for maize variety Japonica (Supplementary Table S1). The search performed through PERL script was refined to select uncharacterized sequences with fewer than 350 amino acid residues.…”

Cyclotides: Overview and Biotechnological Applications

“…[27] For example, database mining approaches were recently for the identification of cyclotide-like sequences in the plant Zea mays (maize), that were later confirmed to be expressed at the mRNA level in the root system of the plant. [30] …”

Structure‐guided identification of antimicrobial peptides in the spathe transcriptome of the non‐model plant, arum lily (Zantedeschia aethiopica)

“…Commonly, AMPs have been identified and studied by traditional purification experiments, screening different targets (Mandal et al., , ; Pinto et al., ). Molecular biology could also be an alternative for this identification (Cunha et al., ; Porto, Miranda, Pinto, Dohms, & Franco, ). However, nowadays, with the reduced costs of next‐generation sequencing technologies, the use of computational data mining approaches for identification of AMPs has become more common (Ganz, ; Porto et al., 2017a).…”

“…Based on this, in a previous work, our group used pattern recognition to find 10 new potential cs‐AMPs in the Z. aethiopica transcriptome (Cândido, Fernandes et al., ). However, in these cases, molecular modeling has been used only as an additional step of validation (Cândido, Fernandes et al., ; Cunha et al., ; Porto et al., ; Silverstein et al., ). Here, we propose the use of threading as the search engine for AMP search instead of an additional step.…”