PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Gueguen, Yannick; Garnier, Julien; Robert, Lilia; Lefranc, Marie‐Paule; Mougenot, Isabelle; DELORGERIL, J; Janech, Michael G.; Gross, Paul S.; Warr, Gregory W.; Cuthbertson, Brandon J.

doi:10.1016/j.dci.2005.04.003

Cited by 154 publications

(93 citation statements)

References 20 publications

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“…Sequences were aligned using DAMBE version 4.5.2 [38,39] and BioEdit version 7.0.5.3 [40]. Amino acid alignment of signal peptide and active domains (PRD and CRD) of each sequence were manually edited according to the respective signature subgroups of PEN-2, PEN-3, PEN-4, ( [15], http://www. penbase.immunaqua.com/), and PEN-5 [25] using DAMBE.…”

Section: Nucleotide Phylogenymentioning

confidence: 99%

Adaptive evolution after duplication of penaeidin antimicrobial peptides

Padhi

Verghese

Otta

et al. 2007

Fish & Shellfish Immunology

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Penaeidin antimicrobial peptides in penaeid shrimps are an important component of their innate immune system that provides immunity against infection caused by several gram-positive bacteria and filamentous fungal species. Despite the knowledge on the identification and characterization of these peptides in penaeid shrimps, little is known about the evolutionary pattern of these peptides and the underlying genetic mechanisms that maintain high sequence diversities in the penaeidin gene family. Based on the phylogenetic analyses and maximum likelihood-based codon substitution analyses, here we present the convincing evidence that multiple copies of penaeidins have evolved by gene duplication, and positive Darwinian selection (adaptive evolution) is the likely cause of accelerated rate of amino acid substitutions among these duplicated genes.While the average ratio of non-synonymous to synonymous substitutions (u) for the entire coding region of both active domains is 0.9805, few codon sites showed significantly higher u (3.73). The likelihood ratio tests that compare models incorporating positive selection (u > 1) at certain codon sites with models not incorporating positive selection (u < 1), failed to reject (p ¼ 0) the evidence of positive Darwinian selection. The rapid adaptive evolution of this gene family might be directed by the pathogens and the faster rate of amino acid substitutions in the N-terminal proline-rich and C-terminal cysteine-rich domains could be due to their direct involvement in the protection against pathogens. When the host expose to different habitats/environment an accelerated rate of amino acid substitutions in both the active domains may also be expected.

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Section: Nucleotide Phylogenymentioning

confidence: 99%

Adaptive evolution after duplication of penaeidin antimicrobial peptides

Padhi

Verghese

Otta

et al. 2007

Fish & Shellfish Immunology

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“…Many bioactive compounds have been investigated predominantly for their antimicrobial, cytotoxic, anti-tumor and anti-inflammatory, antileukemic, antineoplastic and antiviral properties of mollusks [4][5][6][7]. Antibacterial and antiviral activities have been previously reported in the hemolymph of several molluscan species such as sea hares, sea slung, oysters, and mussels [8][9][10][11][12][13][14]. Over recent years, numerous studies on snail mucus composition have clarified many aspects of its properties, although much remains to be investigated on its antibacterial activity.…”

Section: Introductionmentioning

confidence: 99%

Antibacterial and Antifungal Activities of Proteins Extracted from Seven Different Snails

Ulagesan

Kim

2018

Applied Sciences

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Snails have been used both as a food and as a treatment for a variety of medicinal conditions. In this study, seven different snail proteins were evaluated for their antimicrobial activity. Fresh water and land snails of seven different live species were collected and identified. Crude proteins were extracted from seven different snails. The extracted proteins were estimated using Bradford's method and snail proteins were displayed using a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The seven different snail proteins were evaluated for their antimicrobial activity against various pathogenic bacterial and fungal cultures by agar well diffusion method and MIC (Minimum Inhibitory Concentration). One of the most active, crude proteins was from land snail Cryptozona bistrialis and its protein was capable of completely inhibiting the development of pathogenic bacterial and fungal cultures. This study shows that the land snail C. bistrialis proteins could be used as an antibiotic in biomedical research.

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“…The similarity of the crab 6.5kDa protein sequence to penaeidin PRDs (Fig. 1, [40]) implies that there may be other Crustacea that express penaeidin like proteins, but the current definition of penaeidins includes the presence of the CRD as well [36]. Genome studies have yet to reveal clear evidence of how penaeidins evolved relative to other arthropod anti-MP except for the fact that the two domains are encoded by separate exons in some genes [41,42].…”

Section: Overviewmentioning

confidence: 99%

“…Currently two models have been put forth for anti-MP mechanism of action [2,5,33] which are the barrel-like (barrel-stave) pore forming mechanism and the carpeting mechanism. Each of these would result in the compromising of the microbial membrane, and much evidence corroborating both of these mechanisms has been reviewed previously [2,5,33].Penaeidins are antimicrobial peptides from shrimp that are unique in that they are composed of two very different domains [34][35][36], an N-terminal proline-rich domain (PRD) linked to the C-terminal cysteine-rich domain (CRD) [37,38]. While the PRD forms an extended structure, the folded structure of CRD contains an α-helix stabilized by disulfide bonds [37,38].…”

mentioning

confidence: 99%

Diversity in penaeidin antimicrobial peptide form and function

Cuthbertson

Deterding

Williams

et al. 2008

Developmental & Comparative Immunology

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Penaeidins are a diverse family of two-domain antimicrobial peptides expressed in shrimp. Variation in penaeidin sequence results in functional diversity, which was discovered using synthetic reproductions of native penaeidins. An isoform of penaeidin class 3 from L. setiferus (Litset Pen3 −4) was synthesized using native ligation and compared directly with the synthetic penaeidin class 4 known to be expressed in the same organism. New antimicrobial activity data is included in this review that emphasizes differences in effectiveness that are apparent from a direct comparison of two classes. A novel approach to intact penaeidin analysis is presented in the form of Fourier Transform Ion-Cyclotron Resonance Mass Spectrometry, which has implications for the identification of individual penaeidin isoforms without chemical modification or enzymatic cleavage. The new information included in this review helps gather the perspective on relevance of penaeidin diversity to antimicrobial function, the use of synthetic peptides as tools to evaluate specific immune functions and the application of high mass resolution, top-down sequencing methods to the intact analysis of individual penaeidin isoforms. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Keywords NIH Public Access Author ManuscriptDev Comp Immunol. Author manuscript; available in PMC 2009 January 1. Published in final edited form as:Dev Comp Immunol. 2008 ; 32(3): 167-181. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript OverviewAntimicrobial peptides (anti-MPs) are a diverse group of innate immune effector molecules that are utilized by multicellular organisms to prevent or combat infection by microbes. AntiMPs have been the subject of extensive review and several categories of anti-MPs have been described based on structural characteristics with certain themes being repeated throughout the living world [1][2][3][4]. Two prominent themes of anti-MP form that are relevant to this particular review include linear, proline-rich peptides, and cysteine-rich peptides that fold into a tertiary structure stabilized by disulfide bonds. These two separate themes provide a lead-in to the peptide family that is the primary focus of this review, the penaeidin family of anti-MPs.Many examples of short anti-MPs found in the literature contain a considerable percentage of Pro residues associated with other specific amino acids, particularly Arg, in repetitive motifs [5][6][7]. Such peptides have been well characterized in insects and mammals. Apidaecin, abaecin, drosocin, formaecin, pyrrhocoricin and lebo...

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PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Cited by 154 publications

References 20 publications

Adaptive evolution after duplication of penaeidin antimicrobial peptides

Adaptive evolution after duplication of penaeidin antimicrobial peptides

Antibacterial and Antifungal Activities of Proteins Extracted from Seven Different Snails

Diversity in penaeidin antimicrobial peptide form and function

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