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Microbial Genomics logo Microbial Genomics

Volume 9, Issue 12

The mobilome of M247 includes two novel genetic elements: Tn coding for a putative bacteriocin and the siphovirus prophage ΦM247 Open Access

Abstract

is a member of the vaginal and gastrointestinal human microbiota. Here we determined the complete genome sequence of the probiotic strain M247 combining Nanopore and Illumina technologies. The M247 genome is organized in one circular chromosome of 2 336 109 bp, with a GC content of 37.04 % and 2303 ORFs, of which 1962 could be annotated. Analysis of the M247 mobilome, which accounts for 14 % of the whole genome, revealed the presence of: (i) Tn, a novel 14 105 bp long integrative and mobilizable element (IME) containing 16 ORFs; (ii) ΦM247, a novel 42 510 bp long siphovirus prophage containing 52 ORFs; (iii) three clustered regularly interspaced short palindromic repeats (CRISPRs); and (iv) 226 insertion sequences (ISs) belonging to 14 different families. Tn has a modular organization including a mobilization module encoding FtsK homologous proteins and a relaxase, an integration/excision module coding for an integrase and an excisionase, and an adaptation module coding for a class I bacteriocin and homologous to the listeriolysin S () locus of . Genome-wide homology search analysis showed the presence of Tn-like elements in 12 out of 23 . complete public genomes. Mobilization and integration/excision modules are essentially conserved, while the adaptation module is variable since it is the target site for the integration of different ISs. Prophage ΦM247 contains genes for phage structural proteins, DNA replication and packaging, lysogenic and lytic cycles. ΦM247-like prophages are present in seven . complete genomes, with sequence variability mainly due to the integration of ISs. PCR and sequencing showed that the Tn IME excises from the M247 chromosome producing a circular form at a concentration of 4.32×10 copies per chromosome, and reconstitution of the Tn chromosomal target site occurred at 6.65×10 copies per chromosome. The ΦM247 prophage produces an excised form and a reconstituted target site at a level of 3.90×10 and 2.48×10 copies per chromosome, respectively. This study identified two novel genetic elements in . Tn represents the first example of an IME carrying a biosynthetic gene cluster for a class I bacteriocin in .

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  • Accepted:
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Keyword(s): bacteriocins , complete genome , CRISPRs , insertion sequences (ISs) , integrative and mobilization elements (IMEs) , Lactobacillus crispatus , M247 , mobile genetic element (MGEs) , mobilome , nanopore sequencing , probiotic , prophage , siphovirus , Tn7088 and ΦM247
Funding
This study was supported by the:
  • MUR PNRR (Award PE00000007)
    • Principle Award Recipient: FrancescoIannelli
  • MIUR (Award 20177J5Y3P)
    • Principle Award Recipient: FrancescoIannelli
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-12-12
2025-01-26
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/content/journal/mgen/10.1099/mgen.0.001150
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The mobilome of Lactobacillus crispatus M247 includes two novel genetic elements: Tn7088 coding for a putative bacteriocin and the siphovirus prophage ΦM247
M Gen 9, 001150 (2023); https://doi.org/10.1099/mgen.0.001150
/content/journal/mgen/10.1099/mgen.0.001150
/content/journal/mgen/10.1099/mgen.0.001150
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