PhytAMP: a database dedicated to antimicrobial plant peptides

Abstract

Plants produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. Based on amino acid sequence homology, these peptides were classified mostly as α-defensins, thionins, lipid transfer proteins, cyclotides, snakins and hevein-like. Although many antimicrobial plant peptides are now well characterized, much information is still missing or is unavailable to potential users. The compilation of such information in one centralized resource, such as a database would therefore facilitate the study of the potential these peptide structures represent, for example, as alternatives in response to increasing antibiotic resistance or for increasing plant resistance to pathogens by genetic engineering. To achieve this goal, we developed a new database, PhytAMP, which contains valuable information on antimicrobial plant peptides, including taxonomic, microbiological and physicochemical data. Information is very easy to extract from this database and allows rapid prediction of structure/function relationships and target organisms and hence better exploitation of plant peptide biological activities in both the pharmaceutical and agricultural sectors. PhytAMP may be accessed free of charge at http://phytamp.pfba-lab.org.

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

“…A comprehensive database on AMPs with information on their activity would facilitate the study of peptide potential, enabling and promoting sequence-specificity and sequence-activity studies (Hammami et al 2009;Thomas et al 2010). Although many AMPs are now well characterized, much information is still missing or scattered over scientific literature, ie its collection and analysis is troublesome and implies time consuming manual curation.…”

Anionic Host Defence Peptides from the Plant Kingdom: Their Anticancer Activity and Mechanisms of Action

“…Reinforcing this suggestion, theoretical analysis of the peptide showed that it had the potential to adopt -helical structure with a high level of amphiphilicity, indicative of an ability to interact with membranes [31,32]. This molecular architecture is adopted by many other AMPs [13,24,25] and in particular, buforin IIb, which is an -helical CAMP that crosses target membranes to bind DNA and thereby promote anticancer action via the induction of apoptosis [33]. Cr-ACP1 showed similarities to the anticancer action of buforin IIb and was found to have a strong affinity for DNA, which appeared to involve the ability of its charged and polar residues to form a stable hydrogen bond network with DNA nucleotides (Fig.…”

“…These peptides are listed in various databases and are now known to be ubiquitous in plants [13,24,25,[44][45][46] [36] and shows molecular dynamic simulations for the interaction of Cn-AMP2 with a model cancer cell membrane. In this simulation, Cn-AMP2 (TESYFVFSVGM [106]) is in an extended conformation and approaches the surface of the membrane (Fig.…”

“…It is now known that to offset the lack of specialized mobile immune cells possessed by vertebrates, every cell in a plant has the facility to launch an effective immune response, which is mediated by a multi-layered innate immune system that comprises self-surveillance, systemic signalling and chromosomal changes acting in combination to protect against microbial infection and other threats [2,3]. One layer of this immune response involves the production of an arsenal of defence peptides and proteins, which includes: pathogenesisrelated (PR)-proteins [4][5][6][7], recently redefined as 'inducible defence-related proteins [8,9], and host defence peptides (HDPs), whose primary role is a front-line response to microbial infections [10][11][12][13]. On a structural basis, these HDPs can be grouped into the major families: defensins, cyclotides, 2S albumins, lipid transfer proteins, hevein-like proteins knotins, snakins, and glycine-rich proteins [14][15][16][17][18][19][20][21].…”

“…On a structural basis, these HDPs can be grouped into the major families: defensins, cyclotides, 2S albumins, lipid transfer proteins, hevein-like proteins knotins, snakins, and glycine-rich proteins [14][15][16][17][18][19][20][21]. Most of these peptides are cationic (CHPDs), which facilitates theirtoxicity to target cells [10][11][12][13][14][15][16][17][18][19][20][21], but it is becoming increas-*Address correspondence to this author at the Vice Chancellor, London South Bank University, London SE1 0AA; Tel: +44 (0) 20 7815 6001; Fax: +44 (0) 20 7815 6099; E-mail: phoenixd@lsbu.ac.uk ingly clear that plants also produce a number of anionic HDPs (AHDPs) with toxicity to pests, fungi, viruses, bacteria and cancer cells [13,[22][23][24][25][26][27][28]. Currently, the structural / functional relationships underpinning the anticancer and other biological activities of plant AHDPs are poorly understood although, in most cases, the molecular architecture of these peptides has been elucidated [13,22,23,27,28].…”