Broad Phylogenetic Occurrence of the Oxygen-Binding Hemerythrins in Bilaterians

Abstract

Animal tissues need to be properly oxygenated for carrying out catabolic respiration and, as such, natural selection has presumably favored special molecules that can reversibly bind and transport oxygen. Hemoglobins, hemocyanins, and hemerythrins (Hrs) fulfill this role, with Hrs being the least studied. Knowledge of oxygen-binding proteins is crucial for understanding animal physiology. Hr genes are present in the three domains of life, Archaea, Bacteria, and Eukaryota; however, within Animalia, Hrs has been reported only in marine species in six phyla (Annelida, Brachiopoda, Priapulida, Bryozoa, Cnidaria, and Arthropoda). Given this observed Hr distribution, whether all metazoan Hrs share a common origin is circumspect. We investigated Hr diversity and evolution in metazoans, by employing in silico approaches to survey for Hrs from of 120 metazoan transcriptomes and genomes. We found 58 candidate Hr genes actively transcribed in 36 species distributed in 11 animal phyla, with new records in Echinodermata, Hemichordata, Mollusca, Nemertea, Phoronida, and Platyhelminthes. Moreover, we found that "Hrs" reported from Cnidaria and Arthropoda were not consistent with that of other metazoan Hrs. Contrary to previous suggestions that Hr genes were absent in deuterostomes, we find Hr genes present in deuterostomes and were likely present in early bilaterians, but not in nonbilaterian animal lineages. As expected, the Hr gene tree did not mirror metazoan phylogeny, suggesting that Hrs evolutionary history was complex and besides the oxygen carrying capacity, the drivers of Hr evolution may also consist of secondary functional specializations of the proteins, like immunological functions.

Keywords: evolutionay history; metazoa; oxygen-binding protein; transcriptome.

Fig. 1.—

Flow chart of bioinformatics pipeline. Rounded blue rectangles represent input/output files, yellow ovals represent software or scripts, and the green hexagon represents a step which involving manual evaluation. Nineteen metazoan Hrs sequences previous used as query sequences from Genbank (supplementary file 2, Supplementary Material online) were also included in the data set.

Fig. 2.—

Tertiary structure of Hrs from a representative of each newly recorded phylum was inferred using ITASSER (Yang etal. 2015) and confirmed that all sequences have a putative respiratory function and also showed the high similarity among their tertiary structure. Each figure on the right indicated the position of amino acids related to iron binding. (A) Echinodermata—Leptosynapta clarki; (B) Hemichordata—Balanoglossus aurantiaca; (C) Mollusca—Nuculana pernula; (D) Nemertea—Paranemertes peregrina; (E) Phoronida—Phoronis psammophila; (F) Platyhelminthes—Selachomecus olsoni.

Fig. 3.—

Bayesian tree using MrBayes 3.2.1 (Ronquist and Huelsenbeck 2003) midpointed rooted. The blue clade represents cHrs with the five residue deletion between C and D α-helices; gray clades represent clades with protostome myoHr sequences; orange clades represent clades with protostomes and deuterostomes myoHr sequences; green clades represent clades with only deuterostomes myoHr sequences and yellow clades represents sequences of myoHr and “nHr” from a leech and a priapulid. The number after the name of each sequence indicates the GenBank accession numbers for each Hr gene and it is indicated in supplementary file 1, Supplementary Material online.

Fig. 4.—

Hypothesized relationships among metazoan phyla derived from recent phylogenomic studies (Whelan etal. 2015; Halanych 2016; Cannon etal. 2016; Kocot etal. 2017). Pink rectangles represent new Hr records, blue rectangles represent previous records confirmed by our results, and purple rectangle represents exclusively annelid cHrs. MA is metazoan ancestor, BA is bilaterian ancestor, and NA is nephrozoan ancestor.