Molecular selection and functional divergence of HIF-α proteins in vertebrates

The evolutionary and physiological significance of the Hif pathway in teleost fishes

The hypoxia-inducible factor (HIF) pathway is a key regulator of cellular O2 homeostasis and an important orchestrator of the physiological responses to hypoxia (low O2) in vertebrates. Fish can be exposed to significant and frequent changes in environmental O2, and increases in Hif-α (the hypoxia-sensitive subunit of the transcription factor Hif) have been documented in a number of species as a result of a decrease in O2. Here, we discuss the impact of the Hif pathway on the hypoxic response and the contribution to hypoxia tolerance, particularly in fishes of the cyprinid lineage, which includes the zebrafish (Danio rerio). The cyprinids are of specific interest because, unlike in most other fishes, duplicated paralogs of the Hif-α isoforms arising from a teleost-specific genome duplication event have been retained. Positive selection has acted on the duplicated paralogs of the Hif-α isoforms in some cyprinid sub-families, pointing to adaptive evolutionary change in the paralogs. Thus, cyprinids are valuable models for exploring the evolutionary significance and physiological impact of the Hif pathway on the hypoxic response. Knockout in zebrafish of either paralog of Hif-1α greatly reduces hypoxia tolerance, indicating the importance of both paralogs to the hypoxic response. Here, with an emphasis on the cardiorespiratory system, we focus on the role of Hif-1α in the hypoxic ventilatory response and the regulation of cardiac function. We explore the effects of the duration of the hypoxic exposure (acute, sustained or intermittent) on the impact of Hif-1α on cardiorespiratory function and compare relevant data with those from mammalian systems.

Adaptive functional divergence of the warm temperature acclimation-related protein (WAP65) in fishes and the ortholog hemopexin (HPX) in mammals

Gene duplication is an important mechanism that leads to genetic novelty. Different, nonexclusive processes are likely involved, and many adaptive and nonadaptive events may contribute to the maintenance of duplicated genes. In some teleosts, a duplicate copy of the mammalian ortholog Hemopexin (HPX) is present, known as the warm temperature acclimation-related protein (WAP65). Both WAP65 and HPX have been associated with iron homeostasis due to the affinity to bind the toxic-free heme circulating in the blood stream. We have assessed the evolutionary dynamics of WAP65 and HPX genes to understand the adaptive role of positive selection at both nucleotide and amino acid level. Our results showed an asymmetrical evolution between the paralogs WAP65-1 and WAP65-2 after duplication with a slight acceleration of the evolutionary rate in WAP65-1, but not in WAP65-2, and few sites contributing to the functional distinction between the paralogs, whereas the majority of the protein remained under negative selection or relaxed negative selection. WAP65-1 is functionally more distinct from the ancestral protein function than WAP65-2. HPX is phylogenetically closer to WAP65-2 but even so functional divergence was detected between both proteins. In addition, HPX showed a fast rate of evolution when compared with both WAP65-1 and WAP65-2 genes. The assessed 3-dimensional (3-D) structure of WAP65-1 and WAP65-2 suggests that the functional differences detected are not causing noticeable structural changes in these proteins. However, such subtle changes between WAP65 paralogs may be important to understand the differential gene retention of both copies in 20 out of 30 teleosts species studied.