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Unveiling host-parasite relationships through conserved MITEs in prokaryote and viral genomes

Francisco Nadal-Molero1, Riccardo Rosselli1, Silvia Garcia-Juan1

  • 1Department of Physiology, Genetics and Microbiology, University of Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain.

Nucleic Acids Research
|October 29, 2024
PubMed

Insights

Miniature Inverted-repeat Transposable-Elements (MITEs) are widespread in prokaryotic genomes. Their genus-specific distribution offers a novel method for linking microbial hosts to their viruses, revealing new virus-host associations.

Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Transposable elements (TEs) are crucial for genome evolution.
  • Miniature Inverted-repeat Transposable-Elements (MITEs) are non-autonomous TEs found in intergenic regions.
  • MITE mobilization depends on external transposases.

Purpose of the Study:

  • To investigate the prevalence and distribution of MITEs across prokaryotic genomes.
  • To explore the potential of MITEs as markers for virus-host association.
  • To identify novel virus-host relationships using MITEs.

Main Methods:

  • Large-scale analysis of MITEs across nearly 1700 prokaryotic genera and 183,232 genomes.
  • Cluster analysis to determine MITE specificity at genus and species levels.
  • Comparative analysis of MITEs in cellular (cMITEs) and viral (vMITEs) sequences.

Main Results:

  • MITEs were identified in 56.5% of prokaryotic genomes, with over 1.4 million cMITEs found.
  • 97.4% of cMITEs showed genus-specific distribution, and 23% were species-specific.
  • 51,655 cMITEs had counterparts in viral sequences (vMITEs), leading to 379 predicted new host-virus associations, including novel associations in Neisseria and Bacteroidota.

Conclusions:

  • MITEs are broadly distributed in prokaryotic genomes and exhibit significant host specificity.
  • MITEs serve as effective molecular markers for establishing virus-host relationships.
  • This study proposes MITEs as a novel and powerful approach for identifying and validating virus-host associations.

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