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Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain

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Abstract

Antimicrobial peptides (AMPs) are natural antagonistic tools of many bacteria and are considered as attractive antimicrobial agents for the treatment of bacteria with multidrug resistance. Lactic acid bacteria from the gastrointestinal tract of animals and human produce various AMPs inhibiting the growth of pathogens. Here we report the isolation and identification of novel Lactobacillus fermentum strain HF-D1 from the human gut producing AMPs which prevents the growth of P. aeruginosa and S. marcescens. The active fraction of peptides was obtained from the culture liquid by precipitation at 80% saturation of ammonium sulphate. For peptides identification, the precipitate was treated with guanidine hydrochloride to desorb from proteins, separated with ultrafiltration on spin columns with 10,000 MWCO, desalted with a reversed-phase chromatography and subjected to LC–MS/MS analysis. The in silico analysis of the identified 1111 peptides by using ADAM, CAMPR3 and AMPA prediction servers led to identification of the linear peptide with highly probable antimicrobial activity and further investigation of its antibacterial activity mechanism is promising. By using the dereplication algorithm, the peptide highly similar to non-ribosomal cyclic AMPs originally isolated from Staphylococcus epidermidis has been identified. This indicates that L. fermentum HF-D1 represents a novel strain producing antimicrobial peptides targeting P. aeruginosa and S. marcescens.

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Abbreviations

ADAM:

A database of anti-microbial peptides

AMP:

Antimicrobial peptide

BLAST:

Basic local alignment search tool

BLP:

Bacteriocin like peptide

CAMPR3:

Collection of anti-microbial peptides

FA:

Formic acid

FDR:

False discovery rate

fmol:

Femtomole

HPLC:

High performance liquid chromatography

IPC:

Isoelectric point calculator

kDa:

Kilodalton

LAB:

Lactic acid bacteria

LB:

Luria–Bertani

LC–MS/MS:

Liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry

MALDI-TOF:

Matrix assisted laser desorption ionization-time of fight

MASCOT:

Modular approach to software construction operation and test

MGF:

Mascot generic format

MRS:

Man, Rogosa, Sharpe

MS:

Mass spectrometry

MWCO:

Molecular weight cut-off

NCBI:

National center for biotechnology information

NRP:

Non-ribosomal peptide

PBS:

Phosphate-buffered saline

PNP:

Peptidic natural products

RiPP:

Ribosomally synthesized and posttranslationally modified peptides

TFA:

Trifluoroacetic acid

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Funding

This study was funded by the Russian Foundation for Basic Research (Grant Nos. 17-00-00470 (K), 17-00-00456, 17-00-00461, 17-00-00462).

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Authors and Affiliations

  1. Laboratory of Molecular Genetics of Microorganisms, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Street, Kazan, Republic of Tatarstan, Russia, 420008

    Anna S. Pavlova, Georgii D. Ozhegov, Dina R. Yarullina & Airat R. Kayumov

  2. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, Russia, 117997

    Georgij P. Arapidi & Vadim T. Ivanov

  3. Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow, Russia, 119435

    Georgij P. Arapidi, Ivan O. Butenko & Vadim M. Govorun

  4. Moscow Institute of Physics and Technology (State University), Institutskii Per. 9, Dolgoprudny, Moscow Region, Russia, 141700

    Georgij P. Arapidi, Ivan O. Butenko & Vadim M. Govorun

  5. Systems Biology Department, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk, Russia, 630090

    Eduard S. Fomin, Nikolai A. Alemasov & Dmitry A. Afonnikov

  6. Chair of Informational Biology, Novosibirsk State University, 2 Pirogova Str., Novosibirsk, Russia, 630090

    Dmitry A. Afonnikov

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  1. Anna S. Pavlova
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Pavlova, A.S., Ozhegov, G.D., Arapidi, G.P. et al. Identification of Antimicrobial Peptides from Novel Lactobacillus fermentum Strain. Protein J 39, 73–84 (2020). https://doi.org/10.1007/s10930-019-09879-8

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