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Genome Analysis of Two Lichen Bacteriobionts, Lichenibacterium ramalinae and Lichenibacterium minor: Toxin‒Antitoxin Systems and Secretion Proteins

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Abstract

The genomes of two bacteriobionts of the fruticose lichen Ramalina pollinaria, Lichenibacterium ramalinae and L. minor, were analyzed. Genetic determinants potentially determining the integration and adaptation of these bacteria in the lichen thallus were identified. This is the first report on assessment of genetic determinants of the stress reaction factors and secretion systems of lichen bacteriobionts. The genes encoding the proteins of the VapCB toxin–antitoxin (TA) systems exhibited >60% homology with the genes of the known plant symbionts Bradyrhizobium, Sinorhizobium, Agrobacterium, Mesorhizobium, and Ralstonia, as well as with those of a human pathogen Bartonella. The genes encoding the proteins of type II secretion system were found in the genomes of both species. The genes encoding type IV secretion proteins were found only in the genome of L. ramalinae; they were homologous to those of epiphytic Methylobacterium, plant pathogens Agrobacterium, and plant root symbionts Rhizobium and Neorhizobium. Homology between the genes encoding TA system and secretion system proteins and the genes of plant-associated bacteria was over 60%. This may indicate that green algae are the main target for invasion. Detection of the urease synthesis genes in the genomes of lichen bacteriobionts suggested the hypothesis that urea decomposition results in an additional supply of ammonium and bicarbonate to the symbiosis. The latter may potentially be utilized by phototrophic eukaryotes and prokaryotes as an additional carbon source. Analysis of the genomes of lichen bacteriobionts L. ramalinae and L. minor revealed the possible differences in their survival strategies, with L. ramalinae more integrated into the symbiosis, while L. minor is characterized by more autonomous features.

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Funding

This work was supported by the Russian Foundation for Basic Research (project no. 19-04-00297a); it was also supported in part by the Ministry of Science and Higher Education of the Russian Federation.

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  1. Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    T. A. Pankratov

  2. Faculty of Bioengineering and Bioinformatics, Moscow State University, 119192, Moscow, Russia

    P. A. Nikitin

  3. Skryabin Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    E. O. Patutina

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Pankratov, T.A., Nikitin, P.A. & Patutina, E.O. Genome Analysis of Two Lichen Bacteriobionts, Lichenibacterium ramalinae and Lichenibacterium minor: Toxin‒Antitoxin Systems and Secretion Proteins. Microbiology 91, 160–172 (2022). https://doi.org/10.1134/S0026261722020096

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