Poster (download)
Georgii Ozhegov1, Monyr Nait Yahia2, Alexey Vasilchenko3, Natalya Gogoleva4, Dina Yarullina5, Airat Kaumov6
1Kazan Federal University, Kazan, Russia; Perm State Pharmaceutical Academy, Perm, Russia, georgii_provisor@mail.ru
2Kazan Federal University, Kazan, Russia, monyrnait94@gmail.com
3University of Tyumen, Tyumen, Russia, avasilchenko@gmail.com
4Kazan Federal University, Kazan, Russia; Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia, NEGogoleva@kpfu.ru
5Kazan Federal University, Kazan, Russia, kasfes@gmail.com
6Kazan Federal University, Kazan, Russia, kairatr@yandex.ru
Lactobacilli, generally recognized as safe for humans, are characterized with high antagonistic properties. Among 40 strains of Lactobacilli isolated from the faeces of healthy humans, Lactobacillus fermentum HFD1 exhibited significant antimicrobial activity against various nosocomial pathogens. The genome of L.fermentum HFD1 was sequenced on Illumina MiSeq and ONT MinION instruments. After reads assembly 2 circular contigs with respective sizes of 2101878 bp and 5386 bp have been obtained. The raw reads alignment with BWA and post-assembly assessment showed that 99.9% of Illumina reads and 99.2% of MinION reads were mapped to assembled genome. The genome was read with 575x coverage for Illumina data and 454x coverage for MinION data. Based on genome alignment L. fermentum FTDC8312 was found as closest related strain. The BLAST search identified the short contig as similar to bacterophage phiX174. In the genome 2120 coding sequences (CDS) were predicted. Among them 606 were annotated as hypothetical without known biological role. By using CAMPr3, ADAM and AMPA services 5 CDSs with highest summary prediction score were identified as coding for antimicrobial peptides. Further validation of their antimicrobial activity in vitro is required.
Can you characterize 4 CDSs with highest summary prediction score in more details? Have you identified any homology with CDSs in other species that encode protein with antimicrobial activity?
In thesis i put ORF for this CDSs, if you interested I can send it to you.
There are no any homologs in known databases with AntiMicrobial Peptides. Also we try to made synthetic proteins with this amino acids, but they shown no antibacterial activity. Nowadays we work on purifying AMP and determine it aminoacid composition to compare it with ORFs in genome. Maybe it proteins need some specific posttranslation changes and thats why we didn`t find homologs.
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