Computational tools for exploring sequence databases as a resource for antimicrobial peptides

Porto, William F.; Pires, Állan S.; Franco, Octávio L.

doi:10.1016/j.biotechadv.2017.02.001

Cited by 97 publications

(102 citation statements)

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“…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). The use of RegEx should be highlighted among the common computational data mining techniques, and this has been used in a number of works, especially to find cs‐AMP (Cândido, Fernandes et al., ; Cunha et al., ; Porto et al., ; Silverstein et al., ).…”

Section: Discussionmentioning

confidence: 99%

“…Despite the high performance of RegEx, this kind of search identifies sequences by the presence of expressions with fixed, ambiguous, and wildcard characters (Mulvenna et al., ; Porto et al., 2017a; Thompson, ), and for that reason this technique presents a limitation related to the absence of fixed characters (e.g., the initial ZaLTP7 sequence did not present the last cysteine residue, which probably hindered its identification by Cândido, Fernandes et al. ).…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, they have been driving medical science into an unprecedented revolution (Chou, ). Moreover, for AMPs search and their activity prediction, these approaches represent a great advance and increased impact of computational science (Porto et al., 2017a). Further, given the great increase of computational resources and the next‐generation sequencing technologies at reduced costs, the search for cs‐AMPs in transcriptomic and genomic data has become more accessible (Ke et al., ; Porto et al., 2017a; Zhang et al., ).…”

Section: Introductionmentioning

confidence: 99%

“…However, Z. aethiopica , as a non‐model plant, might present peptide sequences which could not be covered by RegEx searches. In that case, a direct use of molecular modeling in data mining seems to be a reasonable alternative (Porto et al., 2017a). Threading techniques predict the secondary structure of a sequence and compare it with experimentally determined structures.…”

Section: Introductionmentioning

confidence: 99%

“…Threading techniques predict the secondary structure of a sequence and compare it with experimentally determined structures. Due to the fact that threading is based on secondary structure, this approach could find structural similarities even in cases of extremely divergent sequences (Gille, Goede, Preißner, Rother, & Frömmel, ; Porto et al., 2017a). Thus, we hypothesized that such approach could be applied to identify new cs‐AMP sequences in transcriptome data, based on structural conservation.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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Antimicrobial peptides (AMPs) are small molecules present in all living beings. Despite their huge sequence variability, AMPs present great structural conservation, mainly in cysteine‐stabilized families. Moreover, in non‐model plants, it is possible to detect cysteine‐stabilized AMPs (cs‐AMPs) with different sequences not covered by conventional searches. Here, we described a threading application for cs‐AMP identification in the non‐model arum lily (Zantedeschia aethiopica) plant, exploring the spathe transcriptome. By using the predicted proteins from the Z. aethiopica transcriptome as our primary source of sequences, we have filtered by using structural alignments of 12 putative cs‐AMP sequences. The two unreported sequences were submitted to PCR validation, and ZaLTP7 gene was confirmed. By using the structure alignments, we classified ZaLTP7 as an LTP type 2‐like. The successful threading application for cs‐AMP identification is an important advance in transcriptomic and proteomic data mining. Besides, the same approach could be applied to the use of NGS public data to discover molecules to combat multidrug‐resistant bacteria.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

et al. 2019

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Strategies toward development of antimicrobial biomaterials for dental healthcare applications

Parhi

Pal

Das

et al. 2021

Biotech & Bioengineering

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Several approaches for elimination of oral pathogens are being explored at the present time since oral diseases remain prevalent affecting approximately 3.5 billion people worldwide. Need for antimicrobial biomaterials in dental healthcare include but is not restricted to designing resin composites and adhesives for prevention of dental caries. Constant efforts are also being made to develop antimicrobial strategies for clearance of endodontic space prior root canal treatment and for treatment of periimplantitis and periodontitis. This article discusses various conventional | © 2021 Wiley Periodicals LLC Microorganisms Type of disease References Lactobacilli Dental caries Caufield et al. (2015) (Mutans streptococci) Streptococcus mutans, Streptococcus sorbinus Dianawati et al. (2020) Aggregatibacter actinomycetemcomitans Periodontitis Oscarsson et al. (2019) Porphyromonas gingivalis Z. He et al. (2020) Fusobacterium nucleatum Endodontic infection Martinho et al. (2016); Matsui et al. (2014) Enterococcus faecalis Alghamdi and Shakir (2020)

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A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications

Ayala-Ruano

Santander-Gordón

Tejera

et al. 2019

Ecology and Evolution

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Streptomyces clavuligerus is a Gram‐positive bacterium that is a high producer of secondary metabolites with industrial applications. The production of antibiotics such as clavulanic acid or cephamycin has been extensively studied in this species; nevertheless, other aspects, such as evolution or ecology, have received less attention. Furthermore, genes that arise from ancient events of lateral transfer have been demonstrated to be implicated in important functions of host species. This approximation discovered relevant genes that genomic analyses overlooked. Thus, we studied the impact of horizontal gene transfer in the S. clavuligerus genome. To perform this task, we applied whole‐genome analysis to identify a laterally transferred sequence from different domains. The most relevant result was a putative antimicrobial peptide (AMP) with a clear origin in the Hymenoptera order of insects. Next, we determined that two copies of these genes were present in the megaplasmid pSCL4 but absent in the S. clavuligerus ATCC 27064 chromosome. Additionally, we found that these sequences were exclusive to the ATCC 27064 strain (and so were not present in any other bacteria) and we also verified the expression of the genes using RNAseq data. Next, we used several AMP predictors to validate the original annotation extracted from Hymenoptera sequences and explored the possibility that these proteins had post‐translational modifications using peptidase cleavage prediction. We suggest that Hymenoptera AMP‐like proteins of S. clavuligerus ATCC 27064 may be useful for both species adaptation and as an antimicrobial molecule with industrial applications.

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Computational tools for exploring sequence databases as a resource for antimicrobial peptides

Cited by 97 publications

References 118 publications

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

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

Strategies toward development of antimicrobial biomaterials for dental healthcare applications

A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications

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