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Journal of Molecular Evolution

, Volume 87, Issue 7–8, pp 254–270 | Cite as

Phylogeny and Evolution of RNA 3′-Nucleotidyltransferases in Bacteria

  • George H. JonesEmail author
Original Article

Abstract

The tRNA nucleotidyltransferases and poly(A) polymerases belong to a superfamily of nucleotidyltransferases. The amino acid sequences of a number of bacterial tRNA nucleotidyltransferases and poly(A) polymerases have been used to construct a rooted, neighbor-joining phylogenetic tree. Using information gleaned from that analysis, along with data from the rRNA-based phylogenetic tree, structural data available on a number of members of the superfamily and other biochemical information on the superfamily, it is possible to suggest a scheme for the evolution of the bacterial tRNA nucleotidyltransferases and poly(A) polymerases from ancestral species. Elements of that scheme are discussed along with questions arising from the scheme which can be explored experimentally.

Keywords

CCA end tRNA Nucleotidyltransferase Poly(A) polymerase Phylogeny Alien index Horizontal gene transfer Polynucleotide phosphorylase 

Notes

Acknowledgements

The author thanks Dr. Shozo Yokoyama for his advice on the phylogenetic analysis and Drs. Yokoyama and Paul Joyce for critical readings of this manuscript. Some of the research described herein was supported by Grant Number MCB-0133520 from the National Science Foundation.

Supplementary material

239_2019_9907_MOESM1_ESM.docx (149 kb)
Figure S1 Word file containing the multiple sequence alignment in CLUSTAL format for the nucleotidyltransferase superfamily members examined in this study (DOCX 149 kb)
239_2019_9907_MOESM2_ESM.tif (16.2 mb)
Figure S2 Maximum likelihood phylogenetic tree constructed as described in Methods. Species names are indicated in color as in Fig. 3 (TIFF 16574 kb)
239_2019_9907_MOESM3_ESM.tif (10 mb)
Figure S3 Alignment of the sequence regions containing the Glu185Gln186/Arg236/Lys232 motif from T. maritima and Synergistetes 53_16. The four amino acids which are involved in the formation of the “springy hinge” are highlighted in red. (TIFF 10235 kb)
239_2019_9907_MOESM4_ESM.tif (19.1 mb)
Figure S4 Models of the CC- and A-adding enzymes from Deinococcus radiodurans and Caldimicrobium thiodismutans. The models were constructed using SWISS-MODEL, from the relevant amino acid sequences and utilized the Thermotoga maritima CCA-adding enzyme as the template (TIFF 19535 kb)
239_2019_9907_MOESM5_ESM.docx (47 kb)
Supplementary material 5 (DOCX 46 kb)

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Authors and Affiliations

  1. 1.Department of BiologyEmory UniversityAtlantaUSA

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