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A plant endophyte Staphylococcus hominis strain MBL_AB63 produces a novel lantibiotic, homicorcin and a position one variant - PubMed

  • ️Fri Jan 01 2021

A plant endophyte Staphylococcus hominis strain MBL_AB63 produces a novel lantibiotic, homicorcin and a position one variant

M Aftab Uddin et al. Sci Rep. 2021.

Abstract

Here we report a jute endophyte Staphylococcus hominis strain MBL_AB63 isolated from jute seeds which showed promising antimicrobial activity against Staphylococcus aureus SG511 when screening for antimicrobial substances. The whole genome sequence of this strain, annotated using BAGEL4 and antiSMASH 5.0 to predict the gene clusters for antimicrobial substances identified a novel antimicrobial peptide cluster that belongs to the class I lantibiotic group. The predicted lantibiotic (homicorcin) was found to be 82% similar to a reported peptide epicidin 280 having a difference of seven amino acids at several positions of the core peptide. Two distinct peaks obtained at close retention times from a RP-HPLC purified fraction have comparable antimicrobial activities and LC-MS revealed the molecular mass of these peaks to be 3046.5 and 3043.2 Da. The presence of an oxidoreductase (homO) similar to that of epicidin 280- associated eciO or epilancin 15X- associated elxO in the homicorcin gene cluster is predicted to be responsible for the reduction of the first dehydrated residue dehydroalanine (Dha) to 2-hydroxypropionate that causes an increase of 3 Da mass of homicorcin 1. Trypsin digestion of the core peptide and its variant followed by ESI-MS analysis suggests the presence of three ring structures, one in the N-terminal and other two interlocking rings at the C-terminal region that remain undigested. Homicorcin exerts bactericidal activity against susceptible cells by disrupting the integrity of the cytoplasmic membrane through pore formation as observed under FE-SEM.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1

Prediction of the homicorcin gene cluster and comparison with other class I lantibiotics. (A) Inhibitory activity of Staphylococcus hominis strain MBL_AB63 (activity overlay assay against Staphylococcus aureus SG511). (B) Biosynthetic gene cluster of different class I lantibiotics. Homicorcin gene cluster was predicted using BAGEL 4.0 (homO: 3-oxoacyl-[acyl-carrier-protein] reductase gene; homI: immunity gene; homA: homicorcin gene; homP: protease gene for leader peptide cleavage; homBC: genes for post translational modification enzyme). (C) Comparisons between the peptide sequences of homicorcin and other class I lantibiotics (residues not similar to Epicidin 280 are shown in red).

Figure 2
Figure 2

Purification of homicorcin through RP-HPLC and mass determination of active peaks by LC–MS. (A) RP-HPLC of active fractions (pooled from ion exchange); Two bioactive (peak-1 and peak-2) fractions were found eluting at 40% and 42% ACN gradient respectively . (B) Strong single peak found in each mass/charge (m/z) state. (C) Mass differences observed between homicorcin and its variant homicorcin 1.

Figure 3
Figure 3

Proposed structure of Homicorcin. (A) Posttranslationally modified residues are indicated as follows: Dha,- dehydroalanine; Dhb—dehydrobutyrine; Abu—aminobutyric acid; Abu-S-Ala -Methyllanthionine; Dha-S-Ala – Lanthionine. The first residue Dha to be modified to 2-hydroxypropionate (Hpo) in homicorcin 1 is shown in a yellow circle. (B) Trypsin digestion sites of homicorcin and identified fragments by LC–MS (Trypsin digestion sites are indicated by (|) and digested fragments of the peptide are marked as A–F). The digested fragments obtained by trypsin digestion are (blue colored box) A- 653.4 Da, B + C- 814.4 Da, D- 357.2 Da, B + C + D- 1153.4 Da, E + F- 1256.6 Da. A’ is the modified N-terminal 2- hydroxypropionate (Hpo) fragment with a molecular mass of 656.4 Da (B).

Figure 4
Figure 4

Antimicrobial mechanism of homicorcin against Staphylococcus simulans 22. Growth inhibition of Staphylococcus simulans 22 was measured as colony forming unit (CFU) count per ml for 148 h in both peptide treated and untreated samples. 8XMIC of homicorcin peptide was applied at mid-log phase.

Figure 5
Figure 5

Electron microscopy of surface morphological changes of bacteria triggered by homicorcin and its variant homicorcin 1. Electron micrographs showing membrane morphology of Micrococcus luteus ATCC 1856 under the following conditions: (A) without treatment, (B) nisin A-treated and (C) homicorcin and (D) homicorcin 1 treated. {Normal cell (green arrow); Pore on cell membrane (red arrow); Lysed cell with deformed cell membrane ( orange arrow)}.

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