Freeze tolerance and the underlying metabolite responses in the Xizang plateau frog, Nanorana parkeri

Effects of hibernation on two important contractile tissues in tibetan frogs, Nanorana parkeri: a perspective from transcriptomics and metabolomics approaches

BACKGROUND

In response to seasonal cold and food shortage, the Xizang plateau frogs, Nanorana parkeri (Anura: Dicroglossidae), enter a reversible hypometabolic state where heart rate and oxygen consumption in skeletal muscle are strongly suppressed. However, the effect of winter hibernation on gene expression and metabolic profiling in these two tissues remains unknown. In the present study, we conducted transcriptomic and metabolomic analyses of heart and skeletal muscle from summer- and winter-collected N. parkeri to explore mechanisms involved in seasonal hibernation.

RESULTS

We identified 2407 differentially expressed genes (DEGs) in heart and 2938 DEGs in skeletal muscle. Enrichment analysis showed that shared DEGs in both tissues were enriched mainly in translation and metabolic processes. Of these, the expression of genes functionally categorized as "response to stress", "defense mechanisms", or "muscle contraction" were particularly associated with hibernation. Metabolomic analysis identified 24 and 22 differentially expressed metabolites (DEMs) in myocardium and skeletal muscle, respectively. In particular, pathway analysis showed that DEMs in myocardium were involved in the pentose phosphate pathway, glycerolipid metabolism, pyruvate metabolism, citrate cycle (TCA cycle), and glycolysis/gluconeogenesis. By contrast, DEMs in skeletal muscle were mainly involved in amino acid metabolism.

CONCLUSIONS

In summary, natural adaptations of myocardium and skeletal muscle in hibernating N. parkeri involved transcriptional alterations in translation, stress response, protective mechanisms, and muscle contraction processes as well as metabolic remodeling. This study provides new insights into the transcriptional and metabolic adjustments that aid winter survival of high-altitude frogs N. parkeri.

Comparative transcriptomic analysis delineates adaptation strategies of Rana kukunoris toward cold stress on the Qinghai-Tibet Plateau

BACKGROUND

Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to understand how the frogs survive in winter.

RESULTS

Transcriptome of liver and muscle of R. kukunoris collected in hibernation and spring were assisted by single molecule real-time (SMRT) sequencing technology. A total of 10,062 unigenes of R. kukunoris were obtained, and 9,924 coding sequences (CDS) were successfully annotated. Our examination of the mRNA response to whole body freezing and recover in the frogs revealed key genes concerning underlying antifreeze proteins and cryoprotectants (glucose and urea). Functional pathway analyses revealed differential regulated pathways of ribosome, energy supply, and protein metabolism which displayed a freeze-induced response and damage recover. Genes related to energy supply in the muscle of winter frogs were up-regulated compared with the muscle of spring frogs. The liver of hibernating frogs maintained modest levels of protein synthesis in the winter. In contrast, the liver underwent intensive high levels of protein synthesis and lipid catabolism to produce substantial quantity of fresh proteins and energy in spring. Differences between hibernation and spring were smaller than that between tissues, yet the physiological traits of hibernation were nevertheless passed down to active state in spring.

CONCLUSIONS

Based on our comparative transcriptomic analyses, we revealed the likely adaptive mechanisms of R. kukunoris. Ultimately, our study expands genetic resources for the freezing-tolerant frogs.

Investigation of seasonal changes in lipid synthesis and metabolism-related genes in the oviduct of Chinese brown frog (<em>Rana dybowskii</em>)

A peculiar physiological characteristic of the Chinese brown frog (Rana dybowskii) is that its oviduct dilates during pre-brumation rather than during the breeding season. This research aimed to examine the expression of genes connected with lipid synthesis and metabolism in the oviduct of R. dybowskii during both the breeding season and pre-brumation. We observed significant changes in the weight and size of the oviduct between the breeding season and pre-brumation. Furthermore, compared to the breeding season, pre-brumation exhibited significantly lower triglyceride content and a marked increase in free fatty acid content. Immunohistochemical results revealed the spatial distribution of triglyceride synthase (Dgat1), triglyceride hydrolase (Lpl and Hsl), fatty acid synthase (Fasn), and fatty acid oxidases (Cpt1a, Acadl, and Hadh) in oviductal glandular cells and epithelial cells during both the breeding season and pre-brumation. While the mRNA levels of triglycerides and free fatty acid synthesis genes (dgat1 and fasn) did not show a significant difference between the breeding season and pre-brumation, the mRNA levels of genes involved in triglycerides and free fatty acid metabolism (lpl, cpt1a, acadl, acox and hadh) were considerably higher during pre-brumation. Furthermore, the R. dybowskii oviduct's transcriptomic and metabolomic data confirmed differential expression of genes and metabolites enriched in lipid metabolism signaling pathways during both the breeding season and pre-brumation. Overall, these results suggest that alterations in lipid synthesis and metabolism during pre-brumation may potentially influence the expanding size of the oviduct, contributing to the successful overwintering of R. dybowskii.

Hepatic transcriptome and gut microbiome provide insights into freeze tolerance in the high-altitude frog, Nanorana parkeri

Among amphibians, freeze tolerance is a low-temperature survival strategy that has been well studied in several species. One influence on animal health and survival under adverse conditions is the gut microbiome. Gut microbes can be greatly affected by temperature fluctuations but, to date, this has not been addressed in high-altitude species. Nanorana parkeri (Anura: Dicroglossidae) lives at high altitudes on the Tibetan plateau and shows a good freeze tolerance. In the present study, we addressed two goals: (1) analysis of the effects of whole body freezing on the liver transcriptome, and (2) assess modifications of the gut microbiome as a consequence of freezing. We found that up-regulated genes in liver were significantly enriched in lipid and fatty acid metabolism that could contribute to accumulating the cryoprotectant glycerol and raising levels of unsaturated fatty acids. The results suggest the crucial importance of membrane adaptations and fuel reserves for freezing survival of these frogs. Down-regulated genes were significantly enriched in the immune response and inflammatory response, suggesting that energy-consuming processes are inhibited to maintain metabolic depression during freezing. Moreover, freezing had a significant effect on intestinal microbiota. The abundance of bacteria in the family Lachnospiraceae was significantly increased after freezing exposure, which likely supports freezing survival of N. parkeri. The lower abundance of bacteria in the family Peptostreptococcaceae in frozen frogs may be associated with the hypometabolic state and decreased immune response. In summary, these findings provide insights into the regulatory mechanisms of freeze tolerance in a high-altitude amphibian at the level of gene expression and gut microbiome, and contribute to enhancing our understanding of the adaptations that support frog survival in high-altitude extreme environments.

Comparative metabolomics analysis reveals high-altitude adaptations in a toad-headed viviparous lizard, Phrynocephalus vlangalii

Extreme environmental conditions at high altitude, such as hypobaric hypoxia, low temperature, and strong UV radiation, pose a great challenge to the survival of animals. Although the mechanisms of adaptation to high-altitude environments have attracted much attention for native plateau species, the underlying metabolic regulation remains unclear. Here, we used a multi-platform metabolomic analysis to compare metabolic profiles of liver between high- and low-altitude populations of toad-headed lizards, Phrynocephalus vlangalii, from the Qinghai-Tibet Plateau. A total of 191 differential metabolites were identified, consisting of 108 up-regulated and 83 down-regulated metabolites in high-altitude lizards as compared with values for low-altitude lizards. Pathway analysis revealed that the significantly different metabolites were associated with carbohydrate metabolism, amino acid metabolism, purine metabolism, and glycerolipid metabolism. Most intermediary metabolites of glycolysis and the tricarboxylic acid cycle were not significantly altered between the two altitudes, but most free fatty acids as well as β-hydroxybutyric acid were significantly lower in the high-altitude population. This may suggest that high-altitude lizards rely more on carbohydrates as their main energy fuel rather than lipids. Higher levels of phospholipids occurred in the liver of high-altitude populations, suggesting that membrane lipids may undergo adaptive remodeling in response to low-temperature stress at high altitude. In summary, this study demonstrates that metabolic profiles differ substantially between high- and low-altitude lizard populations, and that these differential metabolites and metabolic pathways can provide new insights to reveal mechanisms of adaptation to extreme environments at high altitude.

Metabolomic Profiling Reveals Differences in Hypoxia Response between Far Eastern and Siberian Frogs

Anoxia is a significant challenge for most animals, as it can lead to tissue damage and death. Among amphibians, the Siberian frog Rana amurensis is the only known species capable of surviving near-zero levels of oxygen in water for a prolonged period. In this study, we aimed to compare metabolomic profiles of the liver, brain, and heart of the Siberian frog exposed to long-term oxygen deprivation (approximately 0.2 mg/L water) with those of the susceptible Far Eastern frog (Rana dybowskii) subjected to short-term hypoxia to the limits of its tolerance. One of the most pronounced features was that the organs of the Far Eastern frog contained more lactate than those of the Siberian frog despite a much shorter exposure time. The amounts of succinate were similar between the two species. Interestingly, glycerol and 2,3-butanediol were found to be significantly accumulated under hypoxia in the Siberian frog, but not in the Far Eastern frog. The role and biosynthesis of these substances are still unclear, but they are most likely formed in certain side pathways of glycolysis. Based on the obtained data, we suggest a pathway for metabolic changes in the Siberian frog under anoxia.

Integrated analysis of transcriptome and metabolome data reveals insights for molecular mechanisms in overwintering Tibetan frogs, Nanorana parkeri

Nanorana parkeri (Anura, Dicroglossidae) is a unique frog living at high altitude on the Tibetan plateau where they must endure a long winter dormancy at low temperatures without feeding. Here, we presented a comprehensive transcriptomic and metabolomic analysis of liver tissue from summer-active versus overwintering N. parkeri, providing the first broad analysis of altered energy metabolism and gene expression in this frog species. We discovered that significantly up-regulated genes (2,397) in overwintering frogs mainly participated in signal transduction and immune responses, phagosome, endocytosis, lysosome, and autophagy, whereas 2,169 down-regulated genes were mainly involved in metabolic processes, such as oxidation-reduction process, amino acid metabolic process, fatty acid metabolic process, and TCA cycle. Moreover, 35 metabolites were shown to be differentially expressed, including 22 down-regulated and 13 up-regulated in winter. These included particularly notable reductions in the concentrations of most amino acids. These differentially expressed metabolites were mainly involved in amino acid biosynthesis and metabolism. To sum up, these findings suggest that gene expression and metabolic processes show adaptive regulation in overwintering N. parkeri, that contributes to maintaining homeostasis and enhancing protection in the hypometabolic state. This study has greatly expanded our understanding of the winter survival mechanisms in amphibians.

Hayvanlarda Soğuğa Dayanıklılık: Çift Yaşarların Kriyobiyolojisi

Organizmalar yaşamlarını devam ettirebilmek için abiyotik çevresel koşullara uyum sağlarlar. Özellikle ortam sıcaklığındaki değişimler; canlıların beslenme, üreme, gelişim ve morfolojileri üzerinde etkilidir. Sıra dışı sıcaklık değişimleri özellikle ektotermik hayvanlar için ölümcül olabilir. Karasal ektotermler. doğada donma noktasının altındaki sıcaklıklarda hayatta kalabilmek için davranışsal, fizyolojik ve biyokimyasal bazı özel stratejiler geliştirmişlerdir. Bazı türler göç ederek su ya da toprak altında kış uykusuna yatmak suretiyle dondurucu sıcaklıklardan kaçınırlar. Bazıları ise donma koşullarına maruz kalarak kışı geçirmek zorundadırlar. Genel olarak dondurucu soğuğa dayanıklılık donmadan kaçınma (süper soğuma) ve donma toleransı stratejilerine bağlıdır. Donmadan kaçınma durumunda vücut sıvılarının donma noktasının altındaki sıcaklıklarda sıvı formu korunurken donma toleransı stratejisini kullanan canlılarda ise vücutlarındaki toplam suyun %50’sinden fazlasının donması tolere edilebilir. Karasal hibernatör hayvanlardan bazı amfibi ve sürüngen gruplarında da tespit edilen donma toleransı stratejisi onların dondurucu kış koşullarında hayatta kalmalarını sağlamaktadır. Bu özel türler kriyoprotektif mekanizmaları ile donmanın ölümcül etkilerinden korunurlar. Donma süresince yaşamsal faaliyetleri tamamen duran bu hayvanlar çözündükten sonra kısa bir süre içerisinde de normal yaşama dönerler. Bu mucizevi mekanizmanın araştırılması yalnızca hayvanların karmaşık adaptasyonunu açıklamakla kalmaz, aynı zamanda doku ve hücre kriyoprezervasyon teknolojisine de kaynak sağlar. Bu derleme amfibilerin donma toleransı stratejilerine dair bilgiler sunarak henüz yeterince çalışılmamış bu konuda araştırma yapmak isteyenlere katkı sağlayacaktır.

Physiological and Biochemical Adaptations to High Altitude in Tibetan Frogs, Nanorana parkeri

The Xizang plateau frog, N. parkeri (Anura: Dicroglossidae), is endemic to the Tibetan Plateau, ranging from 2,850 to 5,100 m above sea level. The present study explores physiological and biochemical adaptations to high altitude in this species with a particular emphasis on parameters of hematology, oxidative stress, and antioxidant defense in adult and juvenile N. parkeri collected from high (4,600 m a.s.l) and low (3,400 m a.s.l) altitudes. Hematological results showed that hemoglobin concentration ([Hb]), hematocrit (Hct), and red blood cell (RBC) counts were significantly higher in high-altitude N. parkeri. High-altitude juveniles had lower RBC sizes than low-altitude juveniles. Higher levels of GSH and GSSG were indicated only in juveniles from high altitude, not in adults. High-altitude individuals also showed lower oxidative damage, assessed as malondialdehyde (MDA) and carbonyl groups (CG) in the liver. High-altitude adults also showed higher activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX), and glutathione-S-transferase (GST) as well as total antioxidant capacity (T-AOC) in the liver as compared to low-altitude adults. Moreover, higher GPX activity and T-AOC were observed in the heart and brain of high-altitude adults. Liver CAT, GPX, and T-AOC showed significant increases in high-altitude juveniles. Vitamin C content was also higher in the heart of high-altitude frogs compared to low-altitude individuals. In summary, the high-altitude population of N. parkeri showed more robust hematological parameters, less oxidative damage, and stronger antioxidant defenses than the low-altitude population, all contributing to increased protection for survival in high-altitude environments.

Antioxidant and non-specific immune defenses in partially freeze-tolerant Xizang plateau frogs, Nanorana parkeri

The Xizang plateau frog Nanorana parkeri can tolerate brief and partial freezing of their body. To determine the significant role of antioxidant defense and non-specific immune defense in freezing survival of this species, we assayed parameters of oxidative damage, antioxidant defense and non-specific immune enzymes during freezing exposure (-2 °C for 12 h) in five organs (heart, brain, liver, kidney, and skeletal muscle). The results showed that freezing led to a significant rise in the content of malondialdehyde (MDA) and carbonyl groups (CG) in brain, liver and kidney tissues. The activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) increased significantly in brain and liver tissues with an augmentation of total antioxidant capacity (T-AOC). Apparent increments in muscle SOD activity and liver GST activity were also observed during freezing exposure. Vitamin C content significantly decreased in liver and kidney but a significant increase occurred in brain. Activities of non-specific immune enzymes, acid phosphatase (ACP) and alkaline phosphatase (AKP), were also assessed. ACP activity was significantly reduced in all five tissues tested whereas AKP activity decreased significantly in four tissues but rose in brain. In summary, freezing is accompanied by oxidative stress in the high-altitude frog, N. parkeri, as documented by increases in the content of MDA and CG in tissues. Freezing exposure also induced tissue-specific changes in the antioxidant defenses showing that activation of antioxidant systems is a part of the survival strategy of this in a high-altitude frog during freezing. Such up-regulation of antioxidant enzymes suggests a particularly important role for them in the liver and brain, serving as an anticipatory mechanism to deal with the ROS challenge during freeze/thaw episodes. Our findings contribute to extending the current understanding of the mechanisms of freeze tolerance in high-altitude frogs.

Biochemical Response to Freezing in the Siberian Salamander Salamandrella keyserlingii

Simple Summary

The Siberian salamander is a unique amphibian that is capable to survive long-term freezing at −55 °C. We used ¹H-NMR analysis to study quantitative changes of multiple metabolites in liver and hindlimb muscle of the Siberian salamander in response to freezing. For the majority of molecules we observed significant changes in concentrations. Glycerol content in frozen organs was as high as 2% w/w, which confirms its role as a cryoprotectant. No other putative cryoprotectants were detected. Freezing resulted in increased concentrations of glycolysis products: lactate and alanine. Unexpectedly, we detected no increase in concentrations of succinate, which accumulates under ischemia in various tetrapods. Freezing proved to be a dramatic stress with high levels of nucleotide degradation products. There was also significant increase in the concentrations of choline and glycerophosphocholine, which may be interpreted as the degradation of biomembranes. Thus, we found that freezing results not only in macroscopical damage due to ice formation, but also to degradation of DNA and biomembranes.

Abstract

The Siberian salamander Salamandrella keyserlingii Dybowski, 1870 is a unique amphibian that is capable to survive long-term freezing at −55 °C. Nothing is known on the biochemical basis of this remarkable freezing tolerance, except for the fact that it uses glycerol as a low molecular weight cryoprotectant. We used ¹H-NMR analysis to study quantitative changes of multiple metabolites in liver and hindlimb muscle of S. keyserlingii in response to freezing. For the majority of molecules we observed significant changes in concentrations. Glycerol content in frozen organs was as high as 2% w/w, which confirms its role as a cryoprotectant. No other putative cryoprotectants were detected. Freezing resulted in ischemia manifested as increased concentrations of glycolysis products: lactate and alanine. Unexpectedly, we detected no increase in concentrations of succinate, which accumulates under ischemia in various tetrapods. Freezing proved to be a dramatic stress with reduced adenosine phosphate pool and high levels of nucleotide degradation products (hypoxanthine, β-alanine, and β-aminoisobutyrate). There was also significant increase in the concentrations of choline and glycerophosphocholine, which may be interpreted as the degradation of biomembranes. Thus, we found that freezing results not only in macroscopical damage due to ice formation, but also to degradation of DNA and biomembranes.

Metabolic responses of plasma to extreme environments in overwintering Tibetan frogs Nanorana parkeri: a metabolome integrated analysis

Many animals lower their metabolic rate in response to low temperatures and scarcity of food in the winter in phenomena called hibernation or overwintering. Living at high altitude on the Tibetan Plateau where winters are very cold, the frog Nanorana parkeri, survives in one of the most hostile environments on Earth but, to date, relatively little is known about the biochemical and physiological adjustments for overwintering by this species. The present study profiled changes in plasma metabolites of N. parkeri between winter and summer using UHPLC-QE-MS non-target metabolomics in order to explore metabolic adaptations that support winter survival. The analysis showed that, in total, 11 metabolites accumulated and 95 were reduced in overwintering frogs compared with summer-active animals. Metabolites that increased included some that may have antioxidant functions (canthaxanthin, galactinol), act as a metabolic inhibitor (mono-ethylhexylphthalate), or accumulate as a product of anaerobic metabolism (lactate). Most other metabolites in plasma showed reduced levels in winter and were generally involved in energy metabolism including 11 amino acids (proline, isoleucine, leucine, valine, phenylalanine, tyrosine, arginine, tryptophan, methionine, threonine and histidine) and 4 carbohydrates (glucose, citrate, succinate, and malate). Pathway analysis indicated that aminoacyl-tRNA biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis, and nitrogen metabolism were potentially the most prominently altered pathways in overwintering frogs. Changes to these pathways are likely due to fasting and global metabolic depression in overwintering frogs. Concentrations of glucose and urea, commonly used as cryoprotectants by amphibians that winter on land, were significantly reduced during underwater hibernation in N. parkeri. In conclusion, winter survival of the high-altitude frog, N. parkeri was accompanied by substantial changes in metabolomic profiles and this study provides valuable information towards understanding the special adaptive mechanisms of N. parkeri to winter stresses.