Poster abstracts
Poster number 103 submitted by Bianca Lederfeind
Investigating the evolution and prevalence of Homologs of Aquifex aeolicus RNase P (HARP) in the phylum Aquificota
Bianca Lederfeind (Center for RNA Biology, Department of Chemistry and Biochemistry, Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, USA), Gitta Szabo (DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA), Lien B. Lai (Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA), Tanja Woyke (DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA), Venkat Gopalan (Center for RNA Biology, Department of Chemistry and Biochemistry, Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, USA)
Abstract:
RNase P catalyzes removal of the 5'-leader from tRNAs in all domains of life. In most organisms, tRNA 5'-maturation is performed by a catalytic RNA-based ribonucleoprotein (RNP), while in plants, protozoa, and in human mitochondria it is executed by protein-only RNase P (PRORP). An evolutionarily unrelated variant of PRORP termed HARP (Homologs of Aquifex aeolicus RNase P) is present in prokaryotes. While some bacteria have HARP as their only source of RNase P, some archaea have both HARP and the RNP form. It is unknown why a cell would retain both forms, or even more remarkably, forgo the RNA-based mechanism for tRNA 5'-maturation, especially when the protein-based variant is less efficient and less accurate at processing the same precursor-tRNA substrates. One hypothesis is that HARP was selected over the RNP in the phylum Aquificota due to co-evolutionary pressures tied to the organism’s pre-tRNA suite. Support for this expectation emerged from a recent study1 showing that HARP from Aquifex aeolicus prefers A-1 (with RNase P cleavage between N-1 and N+1). Using bioinformatics, we conducted a large-scale survey of Aquificota genomes to assess the presence of RNP and HARP, determine the identity of N-1 and its base-pairing status, identify genomically-encoded CCA, and detect tRNAs in ribosomal RNA operons. We found that the presence of HARP and A-1 preference are not uniform across the phylum: major lineages of Aquificota contain the RNP form instead of HARP and prefer U-1, like other bacteria. The distribution of HARP and RNP among Aquificota suggests that HARP may have replaced RNP function in a subset of Aquificales, resulting in distinct HARP- and RNP-containing lineages within this order. While results from these analyses suggest that it is difficult to identify the underlying evolutionary driving forces, they motivate lines of inquiry that may prove profitable in delineating if HARP or the RNP variant confers a selective advantage under certain conditions.
References:
1 Davydov, S., Wäber, N. B., Gößringer, M., Klemm, P., Rennar, I., Lechner, M., & Hartmann, R. K. (2025). Bacterial/archaeal protein-only RNase P: complementation in Escherichia coli uncovers coevolution of protein-only RNase P and precursor tRNA structures in Aquifex aeolicus. RNA, 31(10), 1503-1522.
Keywords: HARP, bioinformatics