Studies of ribonucleotide reductase in crucian carp-an oxygen dependent enzyme in an anoxia tolerant vertebrate

Still no Rest for the Reductases: Ribonucleotide Reductase (RNR) Structure and Function: An Update

Herein we present a multidisciplinary discussion of ribonucleotide reductase (RNR), the essential enzyme uniquely responsible for conversion of ribonucleotides to deoxyribonucleotides. This chapter primarily presents an overview of this multifaceted and complex enzyme, covering RNR's role in enzymology, biochemistry, medicinal chemistry, and cell biology. It further focuses on RNR from mammals, whose interesting and often conflicting roles in health and disease are coming more into focus. We present pitfalls that we think have not always been dealt with by researchers in each area and further seek to unite some of the field-specific observations surrounding this enzyme. Our work is thus not intended to cover any one topic in extreme detail, but rather give what we consider to be the necessary broad grounding to understand this critical enzyme holistically. Although this is an approach we have advocated in many different areas of scientific research, there is arguably no other single enzyme that embodies the need for such broad study than RNR. Thus, we submit that RNR itself is a paradigm of interdisciplinary research that is of interest from the perspective of the generalist and the specialist alike. We hope that the discussions herein will thus be helpful to not only those wanting to tackle RNR-specific problems, but also those working on similar interdisciplinary projects centering around other enzymes.

Hypoxia Tolerant Species: The Wisdom of Nature Translated into Targets for Stroke Therapy

Human neurons rapidly die after ischemia and current therapies for stroke management are limited to restoration of blood flow to prevent further brain damage. Thrombolytics and mechanical thrombectomy are the available reperfusion treatments, but most of the patients remain untreated. Neuroprotective therapies focused on treating the pathogenic cascade of the disease have widely failed. However, many animal species demonstrate that neurons can survive the lack of oxygen for extended periods of time. Here, we reviewed the physiological and molecular pathways inherent to tolerant species that have been described to contribute to hypoxia tolerance. Among them, Foxo3 and Eif5A were reported to mediate anoxic survival in Drosophila and Caenorhabditis elegans, respectively, and those results were confirmed in experimental models of stroke. In humans however, the multiple mechanisms involved in brain cell death after a stroke causes translation difficulties to arise making necessary a timely and coordinated control of the pathological changes. We propose here that, if we were able to plagiarize such natural hypoxia tolerance through drugs combined in a pharmacological cocktail it would open new therapeutic opportunities for stroke and likely, for other hypoxic conditions.

H2S-producing enzymes in anoxia-tolerant vertebrates: Effects of cold acclimation, anoxia exposure and reoxygenation on gene and protein expression

To lend insight into the potential role of the gasotransmitter hydrogen sulfide (H₂S) in facilitating anoxia survival of anoxia-tolerant vertebrates, we quantified the gene expression of the primary H₂S-synthesizing enzymes, 3-mercaptopyruvate sulfurtransferase (3MST), cystathionine γ-lyase (CSE) and cystathionine β-synthase (CBS), in ventricle and brain of normoxic, anoxic and reoxygenated 21 °C- and 5 °C-acclimated freshwater turtles (Trachemys scripta) and 10 °C-acclimated crucian carp (Carassius carassius). Semi-quantitative Western blotting analysis was also conducted to assess 3MST and CBS protein abundance in ventricle and brain of 5 °C turtles and 10 °C crucian carp subjected to normoxia, anoxia and reoxygenation. We hypothesized that if H₂S was advantageous for anoxia survival, expression levels would remain unchanged or be upregulated with anoxia and/or reoxygenation. Indeed, for both species, gene and protein expression were largely maintained with anoxia exposure (24 h, 21 °C; 5 d, 10 °C; 14 d, 5 °C). With reoxygenation, 3MST expression was increased in turtle and crucian carp brain at the protein and gene level, respectively. Additionally, the effect of cold acclimation on gene expression was assessed in several tissues of the turtle. Expression levels were maintained in most tissues, but decreased in others. The maintenance of gene and protein expression of the H₂S-producing enzymes with anoxia exposure and the up-regulation of 3MST with reoxygenation suggests that H₂S may facilitate anoxic survival of the two champions of vertebrate anoxia survival. The differential effects of cold acclimation on H₂S enzyme expression may influence blood flow to different tissues during winter anoxia.

Re-oxygenation after anoxia induces brain cell death and memory loss in the anoxia-tolerant crucian carp

Crucian carp (Carassius carassius) survive without oxygen for several months, but it is unknown whether they are able to protect themselves from cell death normally caused by the absence, and particularly return, of oxygen. Here, we quantified cell death in brain tissue from crucian carp exposed to anoxia and re-oxygenation using the terminal deoxy-nucleotidyl transferase dUTP nick-end labelling (TUNEL) assay, and cell proliferation by immunohistochemical staining for proliferating cell nuclear antigen (PCNA) as well as PCNA mRNA expression. We also measured mRNA and protein expression of the apoptosis executer protease caspase 3, in laboratory fish exposed to anoxia and re-oxygenation and fish exposed to seasonal anoxia and re-oxygenation in their natural habitat over the year. Finally, a behavioural experiment was used to assess the ability to learn and remember how to navigate in a maze to find food, before and after exposure to anoxia and re-oxygenation. The number of TUNEL-positive cells in the telencephalon increased after 1 day of re-oxygenation following 7 days of anoxia, indicating increased cell death. However, there were no consistent changes in whole-brain expression of caspase 3 in either laboratory-exposed or naturally exposed fish, indicating that cell death might occur via caspase-independent pathways or necrosis. Re-oxygenated crucian carp appeared to have lost the memory of how to navigate in a maze (learnt prior to anoxia exposure), while the ability to learn remained intact. PCNA mRNA was elevated after re-oxygenation, indicating increased neurogenesis. We conclude that anoxia tolerance involves not only protection from damage but also repair after re-oxygenation.

Extreme anoxia tolerance in crucian carp and goldfish through neofunctionalization of duplicated genes creating a new ethanol-producing pyruvate decarboxylase pathway

Without oxygen, most vertebrates die within minutes as they cannot meet cellular energy demands with anaerobic metabolism. However, fish of the genus Carassius (crucian carp and goldfish) have evolved a specialized metabolic system that allows them to survive prolonged periods without oxygen by producing ethanol as their metabolic end-product. Here we show that this has been made possible by the evolution of a pyruvate decarboxylase, analogous to that in brewer's yeast and the first described in vertebrates, in addition to a specialized alcohol dehydrogenase. Whole-genome duplication events have provided additional gene copies of the pyruvate dehydrogenase multienzyme complex that have evolved into a pyruvate decarboxylase, while other copies retained the essential function of the parent enzymes. We reveal the key molecular substitution in duplicated pyruvate dehydrogenase genes that underpins one of the most extreme hypoxic survival strategies among vertebrates and that is highly deleterious in humans.

RRM2B: An oxygen-requiring protein with a role in hypoxia

How tumor cells adapt and survive under hypoxia significantly impacts patient prognosis. We recently demonstrated that the oxygen-requiring ribonucleotide reductase (RNR) enzyme, which provides cells with deoxyribonucleotides, responds to limited oxygen availability by switching small subunits from RRM2 to RRM2B. This property of RNR is essential for hypoxic cell viability and therefore contributes to the most aggressive and therapy-resistant fraction of tumors.

Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication

Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained DNA replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs). However, oxygen is an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us to question the source of dNTPs in hypoxia. Here, we show that the RRM1/RRM2B enzyme is capable of retaining activity in hypoxia and therefore is favored over RRM1/RRM2 in order to preserve ongoing replication and avoid the accumulation of DNA damage. We found two distinct mechanisms by which RRM2B maintains hypoxic activity and identified responsible residues in RRM2B. The importance of RRM2B in the response to tumor hypoxia is further illustrated by correlation of its expression with a hypoxic signature in patient samples and its roles in tumor growth and radioresistance. Our data provide mechanistic insight into RNR biology, highlighting RRM2B as a hypoxic-specific, anti-cancer therapeutic target.

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RRM2B is induced in response to hypoxia in both cell models and patient datasets

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RRM2B retains activity in hypoxic conditions and is the favored RNR subunit in hypoxia

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Loss of RRM2B has detrimental consequences for cell fate, specifically in hypoxia

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RRM2B depletion enhanced hypoxic-specific apoptosis and increased radiosensitivity

Oxygen- and temperature-dependent expression of survival protein kinases in crucian carp (Carassius carassius) heart and brain

Living without oxygen is limited to very few vertebrates, one species being the fresh water fish crucian carp (Carassius carassius), which can survive months of anoxia at low temperatures. Mammalian heart and brain are particularly intolerant to oxygen deprivation, yet these organs can be conditioned to display increased resistance, possibly due to activation of several protein kinases. We hypothesized increased phosphorylation status of these kinases in hypoxic and anoxic crucian carp heart and brain. Moreover, we wanted to investigate whether the kinases showing the strongest phosphorylation during hypoxia/anoxia, ERK 1/2, p38-MAPK, JNK, PKCε, and PKCδ, also had increased expression and phosphorylation at cold temperatures, to better cope with the anoxic periods during winter. We found small differences in the phosphorylation status of ERK 1/2, p38-MAPK, JNK, PKCε, and PKCδ during 10 days of severe hypoxia in both heart and brain (0.3 mg O₂/l) and varying responses to reoxygenation. In contrast, 7 days of anoxia (<0.01 mg O₂/l) markedly increased phosphorylation of ERK 1/2, p38-MAPK, JNK in the heart, and p38-MAPK and PKCε in the brain. Similarly, varying acclimation temperature between 4, 10 and 20°C induced large changes in phosphorylation status. Total protein expression in heart and brain neither changed during different oxygen regimes nor with different acclimation temperatures, except for ERK 1/2, which slightly decreased in the heart at 4°C compared with 20°C. A phylogenetic analysis confirmed that these protein kinases are evolutionarily conserved across a wide range of vertebrate species. Our findings indicate important roles of several protein kinases during oxygen deprivation.

The transcriptomes of the crucian carp complex (Carassius auratus) provide insights into the distinction between unisexual triploids and sexual diploids

Both sexual reproduction and unisexual reproduction are adaptive strategies for species survival and evolution. Unisexual animals have originated largely by hybridization, which tends to elevate their heterozygosity. However, the extent of genetic diversity resulting from hybridization and the genomic differences that determine the type of reproduction are poorly understood. In Carassius auratus, sexual diploids and unisexual triploids coexist. These two forms are similar morphologically but differ markedly in their modes of reproduction. Investigation of their genomic differences will be useful to study genome diversity and the development of reproductive mode. We generated transcriptomes for the unisexual and sexual populations. Genes were identified using homology searches and an ab initio method. Estimation of the synonymous substitution rate in the orthologous pairs indicated that the hybridization of gibel carp occurred 2.2 million years ago. Microsatellite genotyping in each individual from the gibel carp population indicated that most gibel carp genes were not tri-allelic. Molecular function and pathway comparisons suggested few gene expansions between them, except for the progesterone-mediated oocyte maturation pathway, which is enriched in gibel carp. Differential expression analysis identified highly expressed genes in gibel carp. The transcriptomes provide information on genetic diversity and genomic differences, which should assist future studies in functional genomics.