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Volume 10
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10.3390/microorganisms10091720
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Article

A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations

by
Marios Nikolaidis
1,
Andrew Hesketh
2,
Dimitris Mossialos
3,
Ioannis Iliopoulos
4,
Stephen G. Oliver
5 and
Grigorios D. Amoutzias
1,*
1
Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
2
School of Applied Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK
3
Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
4
Division of Basic Sciences, University of Crete Medical School, 71110 Heraklion, Greece
5
Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
*
Author to whom correspondence should be addressed.
Microorganisms 2022, 10(9), 1720; https://doi.org/10.3390/microorganisms10091720
Submission received: 7 June 2022 / Revised: 19 August 2022 / Accepted: 23 August 2022 / Published: 26 August 2022
(This article belongs to the Special Issue Genomics of Bacterial Pathogens)
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Abstract

By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76–82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification.
Keywords: Bacillus subtilis; Bacillus cereus; core proteome; accessory proteome; fingerprints; phylogenomics; comparative genomics; species-specific adaptations; sporulation Bacillus subtilis; Bacillus cereus; core proteome; accessory proteome; fingerprints; phylogenomics; comparative genomics; species-specific adaptations; sporulation

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MDPI and ACS Style

Nikolaidis, M.; Hesketh, A.; Mossialos, D.; Iliopoulos, I.; Oliver, S.G.; Amoutzias, G.D. A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations. Microorganisms 2022, 10, 1720. https://doi.org/10.3390/microorganisms10091720

AMA Style

Nikolaidis M, Hesketh A, Mossialos D, Iliopoulos I, Oliver SG, Amoutzias GD. A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations. Microorganisms. 2022; 10(9):1720. https://doi.org/10.3390/microorganisms10091720

Chicago/Turabian Style

Nikolaidis, Marios, Andrew Hesketh, Dimitris Mossialos, Ioannis Iliopoulos, Stephen G. Oliver, and Grigorios D. Amoutzias. 2022. "A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations" Microorganisms 10, no. 9: 1720. https://doi.org/10.3390/microorganisms10091720

APA Style

Nikolaidis, M., Hesketh, A., Mossialos, D., Iliopoulos, I., Oliver, S. G., & Amoutzias, G. D. (2022). A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations. Microorganisms, 10(9), 1720. https://doi.org/10.3390/microorganisms10091720

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