Predicting Antimicrobial and Other Cysteine-Rich Peptides in 1267 Plant Transcriptomes

Shelenkov, Andrey; Slavokhotova, Anna A.; Одинцова, Т. И.

doi:10.3390/antibiotics9020060

Cited by 15 publications

(22 citation statements)

References 20 publications

(39 reference statements)

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“…Mining of transcriptome databases such as the 1-kp project or publicly available databases provided by NCBI is an emerging field for discovery and analysis of the phylogenetic distribution, sequence diversity, and precursor structure of peptides and proteins. 23 The three most widely used technologies for this task are BLAST-based algorithms, hidden Markov model-based algorithms, and regular expression-based algorithms. As noted by Silverstein et al, cysteine-rich host-defense peptides are often underpredicted by automated annotation programs.…”

Section: Results and Discussionmentioning

confidence: 99%

Discovery of a Beetroot Protease Inhibitor to Identify and Classify Plant-Derived Cystine Knot Peptides

et al. 2020

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Plant peptide protease inhibitors are important molecules in seed storage metabolism and to fight insect pests. Commonly they contain multiple disulfide bonds and are exceptionally stable molecules. In this study, a novel peptide protease inhibitor from beetroot ( Beta vulgaris ) termed bevuTI-I was isolated, and its primary structure was determined via mass spectrometry-based amino acid sequencing. By sequence homology analysis a few peptides with high similarity to bevuTI-I, also known as the Mirabilis jalapa trypsin inhibitor subfamily of knottin-type protease inhibitors, were discovered. Hence, we assessed bevuTI-I for inhibitory activity toward trypsin (IC 50 = 471 nM) and human prolyl oligopeptidase (IC 50 = 11 μM), which is an emerging drug target for neurodegenerative and inflammatory disorders. Interestingly, using a customized bioinformatics approach, bevuTI-I was found to be the missing link to annotate 243 novel sequences of M. jalapa trypsin inhibitor-like peptides. According to their phylogenetic distribution they appear to be common in several plant families. Therefore, the presented approach and our results may help to discover and classify other plant-derived cystine knot peptides, a class of plant molecules that play important functions in plant physiology and are currently being explored as lead molecules and scaffolds in drug development.

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Section: Results and Discussionmentioning

confidence: 99%

Discovery of a Beetroot Protease Inhibitor to Identify and Classify Plant-Derived Cystine Knot Peptides

et al. 2020

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“…There are several reports attributing diverse biological activities to plant-derived CRPs [58][59][60], and in silico analysis such as genome mining has had an important role in CRP discovery [61]. In fact, CRPs have also been found in other organisms, including humans [62] and animals [63,64].…”

Section: Discussionmentioning

confidence: 99%

Isolation of Cysteine-Rich Peptides from Citrullus colocynthis

et al. 2020

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The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant families, such as Cucurbitaceae, are known as a rich source for cysteine-rich peptides, which are gaining importance as valuable pharmaceuticals. In this study, we characterized the C. colocynthis peptidome using chemical modification of cysteine residues, and mass shift analysis via matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. We identified the presence of at least 23 cysteine-rich peptides in this plant, and eight novel peptides, named citcol-1 to -8, with a molecular weight between ~3650 and 4160 Da, were purified using reversed-phase high performance liquid chromatography (HPLC), and their amino acid sequences were determined by de novo assignment of b- and y-ion series of proteolytic peptide fragments. In silico analysis of citcol peptides revealed a high sequence similarity to trypsin inhibitor peptides from Cucumis sativus, Momordica cochinchinensis, Momordica macrophylla and Momordica sphaeroidea. Using genome/transcriptome mining it was possible to identify precursor sequences of this peptide family in related Cucurbitaceae species that cluster into trypsin inhibitor and antimicrobial peptides. Based on our analysis, the presence or absence of a crucial Arg/Lys residue at the putative P1 position may be used to classify these common cysteine-rich peptides by functional properties. Despite sequence homology and the common classification into the inhibitor cysteine knot family, these peptides appear to have diverse and additional bioactivities yet to be revealed.

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“…Based on the sequence and structure similarity, as well as the number and arrangement of cysteine residues in the primary sequence, plant HDPs can be classified into at least eight major families, including defensins, thionins, non-specific lipid-transfer proteins (LTPs), hevein-like peptides, Snakins, knottins, α-hairpinins, and cyclotides [ 1 , 27 ]. A search for potential AMPs in 1267 plant transcriptomes by a computational pipeline resulted in 4849 sequences assigned to the Snakin family, showing that the Snakin family peptide is the most abundant potential AMP that is active against fungal and bacterial pathogens [ 31 ]. Herein, this review is devoted to the novel cysteine-rich plant HDPs families of Snakins, describing the general characters of the Snakin family, as well as the individual features of different family members.…”

Section: Introductionmentioning

confidence: 99%

Molecular and Biological Properties of Snakins: The Foremost Cysteine-Rich Plant Host Defense Peptides

Han

Cao

et al. 2020

JoF

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Plant host defense peptides (HDPs), also known as antimicrobial peptides (AMPs), are regarded as one of the most prevalent barriers elaborated by plants to combat various infective agents. Among the multiple classes of HDPs, the Snakin class attracts special concern, as they carry 12 cysteine residues, being the foremost cysteine-rich peptides of the plant HDPs. Also, their cysteines are present at very highly conserved positions and arranged in an extremely similar way among different members. Like other plant HDPs, Snakins have been shown to exhibit strong antifungal and antibacterial activity against a wide range of plant pathogens. Moreover, they display diversified biological activities in many aspects of plant growth and the development process. This review is devoted to present the general characters of the Snakin class of plant HDPs, as well as the individual features of different Snakin family members. Specifically, the sequence properties, spatial structures, distributions, expression patterns and biological activities of Snakins are described. In addition, further detailed classification of the Snakin family members, along with their possible mode of action and potential applications in the field of agronomy and pathology are discussed.

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Predicting Antimicrobial and Other Cysteine-Rich Peptides in 1267 Plant Transcriptomes

Cited by 15 publications

References 20 publications

Discovery of a Beetroot Protease Inhibitor to Identify and Classify Plant-Derived Cystine Knot Peptides

Discovery of a Beetroot Protease Inhibitor to Identify and Classify Plant-Derived Cystine Knot Peptides

Isolation of Cysteine-Rich Peptides from Citrullus colocynthis

Molecular and Biological Properties of Snakins: The Foremost Cysteine-Rich Plant Host Defense Peptides

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