Comparative genomics in erythropoietic gene discovery: synergisms between the Antarctic icefishes and the zebrafish

Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change

In the frigid, oxygen-rich Southern Ocean (SO), Antarctic icefishes (Channichthyidae; Notothenioidei) evolved the ability to survive without producing erythrocytes and hemoglobin, the oxygen-transport system of virtually all vertebrates. Here, we integrate paleoclimate records with an extensive phylogenomic dataset of notothenioid fishes to understand the evolution of trait loss associated with climate change. In contrast to buoyancy adaptations in this clade, we find relaxed selection on the genetic regions controlling erythropoiesis evolved only after sustained cooling in the SO. This pattern is seen not only within icefishes but also occurred independently in other high-latitude notothenioids. We show that one species of the red-blooded dragonfish clade evolved a spherocytic anemia that phenocopies human patients with this disease via orthologous mutations. The genomic imprint of SO climate change is biased toward erythrocyte-associated conserved noncoding elements (CNEs) rather than to coding regions, which are largely preserved through pleiotropy. The drift in CNEs is specifically enriched near genes that are preferentially expressed late in erythropoiesis. Furthermore, we find that the hematopoietic marrow of icefish species retained proerythroblasts, which indicates that early erythroid development remains intact. Our results provide a framework for understanding the interactions between development and the genome in shaping the response of species to climate change.

Our climate is rapidly changing. To better understand how species can adapt to major climate disturbance, we looked back into the past at a group of fishes that have encountered dramatic climate upheavals and thrived: Antarctic notothenioid fishes. In particular, we focus on the icefishes, which lost the ability to produce red blood cells in the frigid environment of the Southern Ocean. By integrating past climate records with a large genetic dataset of Antarctic fishes, we show that the loss of red blood cells occurred only after sustained cooling of the Southern Ocean. As cooling continued into the modern era, we discover that even some of the “red-blooded” relatives of the icefishes show early genetic and morphological signs of erythrocyte loss. This cooling event left a non-random imprint on the genome of icefishes. With few exceptions, the genetic toolkit underlying red cell development has remained intact in icefishes because many “erythroid” genes perform important functions in other tissues. Rather, mutations have accumulated in gene regulatory regions near genes that control terminal erythroid maturation, such that icefishes continue to produce red cell progenitors but not mature erythrocytes. These results show that the genetic constraints regulating embryonic development shaped the evolutionary response of this fish group to climate change.

A tale of two genes: divergent evolutionary fate of haptoglobin and hemopexin in hemoglobinless antarctic icefishes

Evolution of Antarctic notothenioid fishes in the isolated freezing Southern Ocean have led to remarkable trait gains and losses. One of the most extraordinary was the loss of the major oxygen carrier hemoglobin (Hb) in the icefishes (family Channichthyidae). While the mechanisms of this loss and the resulting compensatory changes have been well studied, the impact of Hb loss on the network of genes that once supported its recycling and disposal has remained unexplored. Here we report the functional fate and underlying molecular changes of two such key Hb-supporting proteins across the icefish family - haptoglobin (Hp) and hemopexin (Hx), crucial in removing cytotoxic free Hb and heme respectively. Hp plays a critical role in binding free Hb for intracellular recycling and absent its primary client, icefish Hp transcription is now vanishingly little and translation into a functional protein is nearly silenced. Hp genotype degeneration has manifested in separate lineages of the icefish phylogeny with three distinct nonsense mutations and a deletion-frameshift, as well as mutated polyadenylation signal sequences. Thus, Hb loss appears to have diminished selective constraint on Hp maintenance, resulting in its stochastic, co-evolutionary drift towards extinction. Hx binds free heme for iron recycling in hepatocytes. In contrast to Hp, Hx genotype integrity is preserved in the icefishes and transcription occurs at comparable levels to the red-blooded notothenioids. The persistence of Hx likely owes to continued selective pressure for its function from mitochondrial and non-Hb cellular hemoproteins.

Divergent Hemogen genes of teleosts and mammals share conserved roles in erythropoiesis: analysis using transgenic and mutant zebrafish

Hemogen is a vertebrate transcription factor that performs important functions in erythropoiesis and testicular development and may contribute to neoplasia. Here we identify zebrafish Hemogen and show that it is considerably smaller (∼22 kDa) than its human ortholog (∼55 kDa), a striking difference that is explained by an underlying modular structure. We demonstrate that Hemogens are largely composed of 21-25 amino acid repeats, some of which may function as transactivation domains (TADs). Hemogen expression in embryonic and adult zebrafish is detected in hematopoietic, renal, neural and gonadal tissues. Using Tol2- and CRISPR/Cas9-generated transgenic zebrafish, we show that Hemogen expression is controlled by two Gata1-dependent regulatory sequences that act alone and together to control spatial and temporal expression during development. Partial depletion of Hemogen in embryos by morpholino knockdown reduces the number of erythrocytes in circulation. CRISPR/Cas9-generated zebrafish lines containing either a frameshift mutation or an in-frame deletion in a putative, C-terminal TAD display anemia and embryonic tail defects. This work expands our understanding of Hemogen and provides mutant zebrafish lines for future study of the mechanism of this important transcription factor.

Summary: Transgenic and mutant zebrafish lines were created to characterize the expression and functions of Hemogen, a transcription factor involved in the formation of red blood cells and other processes.

Beyond the zebrafish: diverse fish species for modeling human disease

In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research.

Neurovascular development in the embryonic zebrafish hindbrain

The brain is made of billions of highly metabolically active neurons whose activities provide the seat for cognitive, affective, sensory and motor functions. The cerebral vasculature meets the brain's unusually high demand for oxygen and glucose by providing it with the largest blood supply of any organ. Accordingly, disorders of the cerebral vasculature, such as congenital vascular malformations, stroke and tumors, compromise neuronal function and survival and often have crippling or fatal consequences. Yet, the assembly of the cerebral vasculature is a process that remains poorly understood. Here we exploit the physical and optical accessibility of the zebrafish embryo to characterize cerebral vascular development within the embryonic hindbrain. We find that this process is primarily driven by endothelial cell migration and follows a two-step sequence. First, perineural vessels with stereotypical anatomies are formed along the ventro-lateral surface of the neuroectoderm. Second, angiogenic sprouts derived from a subset of perineural vessels migrate into the hindbrain to form the intraneural vasculature. We find that these angiogenic sprouts reproducibly penetrate into the hindbrain via the rhombomere centers, where differentiated neurons reside, and that specific rhombomeres are invariably vascularized first. While the anatomy of intraneural vessels is variable from animal to animal, some aspects of the connectivity of perineural and intraneural vessels occur reproducibly within particular hindbrain locales. Using a chemical inhibitor of VEGF signaling we determine stage-specific requirements for this pathway in the formation of the hindbrain vasculature. Finally, we show that a subset of hindbrain vessels is aligned and/or in very close proximity to stereotypical neuron clusters and axon tracts. Using endothelium-deficient cloche mutants we show that the endothelium is dispensable for the organization and maintenance of these stereotypical neuron clusters and axon tracts in the early hindbrain. However, the cerebellum's upper rhombic lip and the optic tectum are abnormal in clo. Overall, this study provides a detailed, multi-stage characterization of early zebrafish hindbrain neurovascular development with cellular resolution up to the third day of age. This work thus serves as a useful reference for the neurovascular characterization of mutants, morphants and drug-treated embryos.

The Antarctic hemoglobinless icefish, fifty five years later: a unique cardiocirculatory interplay of disaptation and phenotypic plasticity

The teleostean Channichthyidae (icefish), endemic stenotherms of the Antarctic waters, perennially at or near freezing, represent a unique example of disaptation among adult vertebrates for their loss of functional traits, particularly hemoglobin (Hb) and, in some species, cardiac myoglobin (Mb), once considered to be essential-life oxygen-binding chromoproteins. Conceivably, this stably frigid, oxygen-rich habitat has permitted high tolerance of disaptation, followed by subsequent adaptive recovery based on gene expression reprogramming and compensatory responses, including an alternative cardio-circulatory design, Hb-free blood and Mb-free cardiac muscle. This review revisits the functional significance of the multilevel cardio-circulatory compensations (hypervolemia, near-zero hematocrit and low blood viscosity, large bore capillaries, increased vascularity with great capacitance, cardiomegaly with very large cardiac output, high blood flow with low systemic pressure and systemic resistance) that counteract the challenge of hypoxemic hypoxia by increasing peripheral oxygen transcellular movement for aerobic tissues, including the myocardium. Reconsidered in the context of recent knowledge on both polar cold adaptation and the new questions related to the advent of nitric oxide (NO) biology, these compensations can be interpreted either according to the "loss-without-penalty" alternative, or in the context of an excessive environmental oxygen supply at low cellular cost and oxygen requirement in the cold. Therefore, rather than reflecting oxygen limitation, several traits may indicate structural overcompensation of oxygen supply reductions at cell/tissue levels. At the multilevel cardio-circulatory adjustments, NO is revealing itself as a major integrator, compensating disaptation with functional phenotypic plasticity, as illustrated by the heart paradigm. Beside NOS-dependent NO generation, recent knowledge concerning Hb/Mb interplay with NO and nitrite has revealed unexpected functions in addition to the classical respiratory role of these proteins. In fact, nitrite, a major biologic reservoir of NO, generates it through deohyHb- and deoxyMb-dependent nitrite reduction, thereby regulating hypoxic vasodilation, cellular respiration and signalling. We suggest that both Hb and Mb are involved as nitrite reductases under hypoxic conditions in a number of cardiocirculatory processes. On the whole, this opens new horizons in environmental and evolutionary physiology.

Evolutionary mutant models for human disease

Although induced mutations in traditional laboratory animals have been valuable as models for human diseases, they have some important limitations. Here, we propose a complementary approach to discover genes and mechanisms that might contribute to human disorders: the analysis of evolutionary mutant models in which adaptive phenotypes mimic maladaptive human diseases. If the type and mode of action of mutations favored by natural selection in wild populations are similar to those that contribute to human diseases, then studies in evolutionary mutant models have the potential to identify novel genetic factors and gene-by-environment interactions that affect human health and underlie human disease.

Molecular ecophysiology of Antarctic notothenioid fishes

The notothenioid fishes of the Southern Ocean surrounding Antarctica are remarkable examples of organismal adaptation to extreme cold. Their evolution since the mid-Miocene in geographical isolation and a chronically cold marine environment has resulted in extreme stenothermality of the extant species. Given the unique thermal history of the notothenioids, one may ask what traits have been gained, and conversely, what characters have been lost through change in the information content of their genomes. Two dramatic changes that epitomize such evolutionary transformations are the gain of novel antifreeze proteins, which are obligatory for survival in icy seawater, by most notothenioids and the paradoxical loss of respiratory haemoproteins and red blood cells, normally deemed indispensable for vertebrate life, by the species of a highly derived notothenioid family, the icefishes. Here, we review recent advances in our understanding of these traits and their evolution and suggest future avenues of investigation. The formerly coherent paradigm of notothenioid freeze avoidance, developed from three decades of study of antifreeze glycoprotein (AFGP) based cold adaptation, now faces challenges stemming from the recent discovery of antifreeze-deficient, yet freeze-resistant, early notothenioid life stages and from definitive evidence that the liver is not the physiological source of AFGPs in notothenioid blood. The resolution of these intriguing observations is likely to reveal new physiological traits that are unique to the notothenioids. Similarly, the model of AFGP gene evolution from a notothenioid pancreatic trypsinogen-like gene precursor is being expanded and refined based on genome-level analyses of the linked AFGP loci and their ancestral precursors. Finally, the application of comparative genomics to study evolutionary change in the AFGP genotypes of cool-temperate notothenioids from sub-Antarctic habitats, where these genes are not necessary, will contribute to the mechanistic understanding of the dynamics of AFGP gene gain and loss. In humans and most vertebrates, mutations in the alpha- or beta-globin genes or defects in globin chain synthesis are causes of severe genetic disease. Thus, the 16 species of haemoglobinless, erythrocyte-null icefishes are surprising anomalies -- in fact, they could only have evolved and thrived due to relaxed selection pressure for oxygen-binding proteins in the cold, oxygen-rich waters of the Southern Ocean. Fifteen of the sixteen icefish species have lost most of the adult alphabeta-globin locus and retain only a small 3' fragment of the alpha-globin gene. The only exception to this pattern occurs in Neopagetopsis ionah, which possesses a disrupted alphabeta-globin gene complex that probably represents a non-functional intermediate on the evolutionary pathway to near total globin gene extinction. By contrast, six of the icefish species fail to express myoglobin. The absence of myoglobin expression has occurred by several independent mutations and distinct mechanisms. Haemoprotein loss is correlated with dramatic increases in cellular mitochondrial density, heart size, blood volume and capillary bed volume. Evolution of these compensatory traits was probably facilitated by the homeostatic activity of nitric oxide, a key modulator of angiogenesis and mitochondrial biogenesis. These natural knockouts of the red blood cell lineage are an excellent genomic resource for erythroid gene discovery by comparative genomics, as illustrated for the newly described gene, bloodthirsty.