Figure 1. Two evolutionary scenarios for TPRs, illustrated by neighbor-joining phylogenetic trees.

(a) Amplification from single helical hairpin, as seen in TPR proteins from Cyanobacteria. (b) Divergent evolution of a TPR with multiple repeat units, as seen in the TPR domains of Serine/threonine-protein phosphatase 5 (Ara: Arabidopsis thaliana, Dan: Danio rerio, Hom: Homo sapiens, Mus: Musca domestica, Sac: Saccharomyces cerevisiae, The: Theileria annulata, Xen: Xenopus (Silurana) tropicalis). Since evolutionary reconstructions are subject to Occam’s razor and reflect the hypothesis with the fewest assumptions, we have postulated here one amplification event from one precursor hairpin. Our findings would however also be fully compatible with the precursor hairpin yielding a population of homologous variants, some of which were independently amplified to TPR-like folds; one or more survivors among these would have become the ancestor(s) of today’s TPR proteins. In this more complex scenario, the homology of TPR proteins, which we trace through the comparison of individual hairpins, is still given, but the TPR fold could have arisen from several independent amplifications, and not just a single one.

DOI: http://dx.doi.org/10.7554/eLife.16761.003

Figure 1—figure supplement 1. Multiple sequence alignments of recently amplified TPR repeat units.

(a) Alignments of the TPR units used for the phylogeny in Figure 1a. Residues different from the most common one in each column are shown in bold face and highlighted in yellow. Abbreviations: Ana: Anabaena sp. 90 (gi: 752818954, accession: WP_041458168.1); Cal: Calothrix sp. 336/3 (gi: 821031795, accession: WP_046815017.1); Cya: Cyanothece sp. PCC 8801 (gi: 501590504, accession: WP_012594639.1); fil: filamentous cyanobacterium ESFC-1 (gi: 740500649, accession: WP_038331513.1); Mic: Microcystis aeruginosa SPC777 (gi: 513477764, accession: EPF24195.1). (b) The corresponding alignment of the DNA sequences for the most recently amplified TPR units, Cal4-Cal18, of which the central repeats, Cal9-Cal16, are fully identical. Synonymous mutations (highlighted in gray) are found at less than 1% of the nucleotides, illustrating the recent time point of the amplification. Non-synonymous mutations (highlighted in yellow) are about 2.5 times as frequent as synonymous ones.

DOI: http://dx.doi.org/10.7554/eLife.16761.004

Figure 1—figure supplement 2. Multiple sequence alignments of the three TPR repeat units in serine/threonine-protein phosphatase 5 from seven taxa.

Columns with identify ≥80% are highlighted in black and marked by vertical bars (|); column with identify <80% but ≥50% are highlighted in gray and marked by dots (.). Abbreviations: Ara: Arabidopsis thaliana (gi: 18406066, accession: NP_565985.1); Dan: Danio rerio (gi: 126158897, accession: NP_001014372.2); Hom: Homo sapiens (gi: 5453958, accession: NP_006238.1); Mus: Musca domestica (gi: 557765703, accession: XP_005182549.1); Sac: Saccharomyces cerevisiae S288c (gi: 398365781, accession: NP_011639.3); The: Theileria annulata strain Ankara (gi: 84994100, accession: XP_951772.1); Xen: Xenopus tropicalis (gi: 56118654, accession: NP_001007891.1).

DOI: http://dx.doi.org/10.7554/eLife.16761.005