Ribosomal proteins could explain the phylogeny of Bacillus species

Abstract

Protein translation is a highly conserved process in biology. As participants of translation, ribosomal proteins in the large and small subunits of the ribosomes are likely to be highly conserved; thus, could they be endowed with sufficient sequence diversity to chronicle the evolutionary history of different species in the same or different genus? Using different Bacillus species as a model system, this study sought to examine if ribosomal proteins could reproduce the maximum likelihood phylogeny described by 16S rRNA of the investigated Bacillus species. Bacillus species investigated were Bacillus amyloliquefaciens, Bacillus cereus, Bacillus licheniformis, Bacillus megaterium, Bacilluspumilus, Bacillus subtilis, and Bacillus thuringiensis. Results revealed that ribosomal proteins could be categorized into four different groups depending on their extent in reproducing the 16S rRNA phylogeny of the different Bacillus species. The first group comprises ribosomal protein that could reproduce all the phylogenetic positions of the Bacillus species accurately. These ribosomal proteins were ribosomal protein L6, L7/12, L9, L13, L24, L32, S3, S9, S12, S15, S16, S17, and S18. Ribosomal proteins that hold partial phylogenetic significance constitutes the second group where the ribosomal proteins could reproduce the major branches of the 16S rRNA phylogenetic tree but differ in the placement of one or two Bacillus species. In general, this group of ribosomal proteins had difficulty differentiating B. licheniformis and B. pumilus at the sequence level. Members of this group of ribosomal protein include ribosomal protein L22, L29, L30, L31 Type B, L33, L35, S1, S4, S5, S6, S7, S8, S11, S13, S19, and S20. The third group of ribosomal proteins were those which were highly conserved at the sequence level, and which could not differentiate the different Bacillus species. These ribosomal proteins were ribosomal protein L5, L36, S2, S10, and S21. Finally, there were also ribosomal proteins that randomly placed the different Bacillus species into phylogenetic positions not in sync with those depicted by the 16S rRNA phylogenetic tree. These ribosomal proteins were ribosomal protein L7Ae, L17, L20, L23, L27, L28, L31, L34 and S14 Type Z. Overall, members of all four groups of ribosomal proteins came from both the large and small ribosome subunits which meant that evolutionary forces exerted selective pressure on both subunits but at differing extents. Collectively, specific ribosomal proteins could reproduce the phylogeny of different Bacillus species as described by the gold standard phylogenetic marker, 16S rRNA, which highlighted that co-evolutionary processes could be at work in shaping the evolution of ribosomal proteins and rRNA in close contact with each other in the ribosome. Subject areasecology, biochemistry, biotechnology, microbiology, cell biology Significance of the work16S rRNA is the gold standard phylogenetic marker used to inform the evolutionary relationships between different species across the three domains of life. Given that 16S rRNA is nestled in the ribosomes together with a consortium of ribosomal proteins each with unique structural and enzymatic functions, could ribosomal proteins be used similarly as phylogenetic markers for informing species divergence and relationships? Specifically, as part of the highly conserved ribosome important to protein translation, do ribosomal proteins possess sufficient sequence diversity to help chronicle the evolutionary relationships between different species? By reconstructing the maximum likelihood phylogenetic tree of different Bacillus species, this study revealed that ribosomal proteins fall into four categories concerning their utility for informing phylogeny between different species of the same genus. Specifically, there existed ribosomal proteins able to accurately reproduce the phylogenetic tree described by 16S rRNA. On the other hand, there were ribosomal proteins that hold only partial phylogenetic significance where they could reproduce the major branches of the reference phylogenetic tree but differ in the placement of one or two species along the tree. Besides the above two categories, they were also ribosomal proteins whose sequence diversity was not sufficient to help differentiate between different Bacillus species. Finally, another class of ribosomal proteins did not chronicle the evolutionary trajectories of the different species resulting in phylogenetic tree with random placement of the different species. Overall, evolutionary forces likely exerted different selection forces on different ribosome subunits as well as individual ribosomal protein that resulted in the differentiation of their utility as phylogenetic markers of different species of the same genus. Co-evolution between ribosomal proteins as well as between ribosomal proteins and rRNA might underpin part of the evolutionary history chronicled by individual ribosomal proteins, thereby, endowing them with phylogenetic significance. HighlightsO_LIRibosomal proteins were found to be useful in describing the phylogeny of different Bacillus species compared to the gold standard phylogenetic marker, 16S rRNA. C_LIO_LIBy examining the maximum likelihood phylogenetic tree reconstructed, ribosomal proteins could be categorized into four groups with differing phylogenetic significance. C_LIO_LIThe first group comprises ribosomal proteins able to accurately reproduce all the phylogenetic positions of different Bacillus species relative to 16S rRNA phylogenetic tree. This group include ribosomal protein L6, L7/12, L9, L13, L24, L32, S3, S9, S12, S15, S16, S17, and S18. C_LIO_LIThe second group refers to ribosomal proteins able to reproduce the major branches of the 16S rRNA phylogenetic tree but lacks in the correct placement of one or two Bacillus species. These ribosomal proteins were L22, L29, L30, L31 Type B, L33, L35, SI, S4, S5, S6, S7, S8, Sll, S13, S19, and S20. C_LIO_LIThe third group of ribosomal proteins are ones with highly conserved sequence unable to differentiate between different Bacillus species. It comprised ribosomal proteins L5, L36, S2, S10, and S21. C_LIO_LIThe final group of ribosomal proteins did not chronicle the evolutionary forces acting on the different Bacillus species and generated phylogenetic trees with random placement of the different Bacillus species. These ribosomal proteins were L7Ae, L17, L20, L23, L27, L28, L31, L34 and S14 Type Z. C_LI