Abstract
The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.
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BR duly acknowledges the grant received from the University Grants Commission, New Delhi, India (Letter no. PDFSS-2013-14-ST-MAH-4350).
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This article is funded by University Grants Commission, PDFSS-2013-14-ST-MAH-4350.
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BNR: conceptualization, methodology, validation, formal analysis, investigation, data curation, visualization, writing - original draft, writing - review and editing. YSS and KJ: supervision, resources, methodology, project administration, writing - review and editing. All authors have reviewed and finalized this manuscript.
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Rekadwad, B.N., Shouche, Y.S. & Jangid, K. Investigation of tRNA-based relatedness within the Planctomycetes−Verrucomicrobia−Chlamydiae (PVC) superphylum: a comparative analysis. Arch Microbiol 205, 366 (2023). https://doi.org/10.1007/s00203-023-03694-7
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DOI: https://doi.org/10.1007/s00203-023-03694-7