Significant modulation of the hepatic proteome induced by exposure to low temperature in Xenopus laevis

miR-2a and miR-279 are functionally associated with cold tolerance in Dermacentor silvarum (Acari: Ixodidae)

Ticks are obligate blood-sucking ectoparasites that can attack mammals, birds, reptiles as well as amphibians. Dermacentor silvarum, an important vector of various pathogenic bacteria, viruses, and protozoans, is widely distributed in China. MicroRNAs (miRNAs) are ~22 nucleotide non-coding small RNA molecules, involved in the regulation of various physiological and cellular processes. Previous studies demonstrated the vital roles of miRNAs during the reproduction and development of ticks, whereas, the regulatory/functional roles of microRNAs during the cold response of ticks remain unexplored. Here, we identified and functionally explored D. silvarum miRNAs involved in cold response to gain further understanding of the molecular regulatory mechanisms underlying cold stress in ticks. The microRNA libraries of D. silvarum were established via high-throughput sequencing after exposure to different cold treatments. A total of 147 miRNAs, including 44 known miRNAs and 103 new miRNAs, were identified. The verification of six highly differentially expressed miRNAs (miR-2a, miR-5305, miR-7, miR-279, miR-993, and novel-3) via RT-qPCR were consistent with the high-throughput sequence results. miR-2a peaked by day 6 and miR-279 expression was lowest by day 3 after cold treatment. The potential target genes of miR-2a and miR-279 were the glycogen phosphorylase (GPase) gene and serine gene, respectively. After injecting D. silvarum ticks with miR-2a and miR-279 antagonists, their respective target genes were up-regulated and vice-versa after injection with the agonists. These results indicated that these two miRNAs and their target genes may be involved in the cold response of D. silvarum ticks.

Transcriptomic Changes in Hot Spring Frog Tadpoles (Buergeria otai) in Response to Heat Stress

Buergeria frog tadpoles exhibit high thermal tolerance and are occasionally found in water pools that temporarily exceed 40°C. With the aim of understanding how they can cope with the severe heat stress, we performed RNA-seq of three heat-treated (38°C) and three control (25°C) tadpoles and compared their transcriptomic profiles. We identified 382 differentially expressed transcripts. A protein-protein interaction (PPI) network analysis of these transcripts further identified hub proteins involved in protein degradation, stress granule assembly, and global suppression of DNA transcription and mRNA translation. Along with the avoidance behavior against high water temperature, these endurance mechanisms potentially support tadpoles to survive in high temperatures for short periods of time. Similar mechanisms may exist in many other amphibian species whose habitats are prone to high temperatures.

Thyroid Hormone Receptor Is Essential for Larval Epithelial Apoptosis and Adult Epithelial Stem Cell Development but Not Adult Intestinal Morphogenesis during Xenopus tropicalis Metamorphosis

Vertebrate postembryonic development is regulated by thyroid hormone (T3). Of particular interest is anuran metamorphosis, which offers several unique advantages for studying the role of T3 and its two nuclear receptor genes, TRα and TRβ, during postembryonic development. We have recently generated TR double knockout (TRDKO) Xenopus tropicalis animals and reported that TR is essential for the completion of metamorphosis. Furthermore, TRDKO tadpoles are stalled at the climax of metamorphosis before eventual death. Here we show that TRDKO intestine lacked larval epithelial cell death and adult stem cell formation/proliferation during natural metamorphosis. Interestingly, TRDKO tadpole intestine had premature formation of adult-like epithelial folds and muscle development. In addition, T3 treatment of premetamorphic TRDKO tadpoles failed to induce any metamorphic changes in the intestine. Furthermore, RNA-seq analysis revealed that TRDKO altered the expression of many genes in biological pathways such as Wnt signaling and the cell cycle that likely underlay the inhibition of larval epithelial cell death and adult stem cell development caused by removing both TR genes. Our data suggest that liganded TR is required for larval epithelial cell degeneration and adult stem cell formation, whereas unliganded TR prevents precocious adult tissue morphogenesis such as smooth-muscle development and epithelial folding.

Analysis of Thyroid Hormone Receptor α-Knockout Tadpoles Reveals That the Activation of Cell Cycle Program Is Involved in Thyroid Hormone-Induced Larval Epithelial Cell Death and Adult Intestinal Stem Cell Development During Xenopus tropicalis Metamorphosis

Background: There are two highly conserved thyroid hormone (triiodothyronine [T3]) receptor (TR) genes, TRα and TRβ, in all vertebrates, and the expression of TRα but not TRβ is activated earlier than T3 synthesis during development. In human, high levels of T3 are present during the several months around birth, and T3 deficiency during this period causes severe developmental abnormalities including skeletal and intestinal defects. It is, however, difficult to study this period in mammals as the embryos and neonates depend on maternal supply of nutrients for survival. However, Xenopus tropicalis undergoes a T3-dependent metamorphosis, which drastically changes essentially every organ in a tadpole. Of interest is intestinal remodeling, which involves near complete degeneration of the larval epithelium through apoptosis. Concurrently, adult intestinal stem cells are formed de novo and subsequently give rise to the self-renewing adult epithelial system, resembling intestinal maturation around birth in mammals. We have previously demonstrated that T3 signaling is essential for the formation of adult intestinal stem cells during metamorphosis. Methods: We studied the function of endogenous TRα in the tadpole intestine by using knockout animals and RNA-seq analysis. Results: We observed that removing endogenous TRα caused defects in intestinal remodeling, including drastically reduced larval epithelial cell death and adult intestinal stem cell proliferation. Using RNA-seq on intestinal RNA from premetamorphic wild-type and TRα-knockout tadpoles treated with or without T3 for one day, before any detectable T3-induced cell death and stem cell formation in the tadpole intestine, we identified more than 1500 genes, which were regulated by T3 treatment of the wild-type but not TRα-knockout tadpoles. Gene Ontology and biological pathway analyses revealed that surprisingly, these TRα-regulated genes were highly enriched with cell cycle-related genes, in addition to genes related to stem cells and apoptosis. Conclusions: Our findings suggest that TRα-mediated T3 activation of the cell cycle program is involved in larval epithelial cell death and adult epithelial stem cell development during intestinal remodeling.

Hepatic transcriptome of the freeze-tolerant Cope's gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing

Background

Cope’s gray treefrog, Dryophytes chrysoscelis, withstands the physiological challenges of corporeal freezing, partly by accumulating cryoprotective compounds of hepatic origin, including glycerol, urea, and glucose. We hypothesized that expression of genes related to cryoprotectant mobilization and stress tolerance would be differentially regulated in response to cold. Using high-throughput RNA sequencing (RNA-Seq), a hepatic transcriptome was generated for D. chrysoscelis, and gene expression was compared among frogs that were warm-acclimated, cold-acclimated, and frozen.

Results

A total of 159,556 transcripts were generated; 39% showed homology with known transcripts, and 34% of all transcripts were annotated. Gene-level analyses identified 34,936 genes, 85% of which were annotated. Cold acclimation induced differential expression both of genes and non-coding transcripts; freezing induced few additional changes. Transcript-level analysis followed by gene-level aggregation revealed 3582 differentially expressed genes, whereas analysis at the gene level revealed 1324 differentially regulated genes. Approximately 3.6% of differentially expressed sequences were non-coding and of no identifiable homology. Expression of several genes associated with cryoprotectant accumulation was altered during cold acclimation. Of note, glycerol kinase expression decreased with cold exposure, possibly promoting accumulation of glycerol, whereas glucose export was transcriptionally promoted by upregulation of glucose-6-phosphatase and downregulation of genes of various glycolytic enzymes. Several genes related to heat shock protein response, DNA repair, and the ubiquitin proteasome pathway were upregulated in cold and frozen frogs, whereas genes involved in responses to oxidative stress and anoxia, both potential sources of cellular damage during freezing, were downregulated or unchanged.

Conclusion

Our study is the first to report transcriptomic responses to low temperature exposure in a freeze-tolerant vertebrate. The hepatic transcriptome of Dryophytes chrysoscelis is responsive to cold and freezing. Transcriptomic regulation of genes related to particular pathways, such as glycerol biosynthesis, were not all regulated in parallel. The physiological demands associated with cold and freezing, as well as the transcriptomic responses observed in this study, are shared with several organisms that face similar ecophysiological challenges, suggesting common regulatory mechanisms. The role of transcriptional regulation relative to other cellular processes, and of non-coding transcripts as elements of those responses, deserve further study.

Comprehensive RNA-Seq analysis of notochord-enriched genes induced during Xenopus tropicalis tail resorption

Anuran metamorphosis is perhaps the most dramatic developmental process regulated by thyroid hormone (TH). One of the unique processes that occur during metamorphosis is the complete resorption of the tail, including the notochord. Interestingly, recent gene knockout studies have shown that of the two known vertebrate TH receptors, TRα and TRβ, TRβ appears to be critical for notochord regression during tail resorption in Xenopus tropicalis. To determine the mechanisms underlying notochord regression, we carried out a comprehensive gene expression analysis in the notochord during metamorphosis by using RNA-Seq analyses of whole tail at stage 60 before any noticeable tail length reduction, whole tail at stage 63 when the tail length is reduced by about one half, and the rest of the tail at stage 63 after removing the notochord. This allowed us to identify many notochord-enriched, metamorphosis-induced genes at stage 63. Future studies on these genes should help to determine if they are regulated by TRβ and play any roles in notochord regression.

iTRAQ-based quantitative proteomic analysis of Takifugu fasciatus liver in response to low-temperature stress

Low temperatures profoundly influence the physiological and behavioural processes of ectotherms, especially teleosts, which have made them the subjects of strong interest over time. However, the characteristics of fish cold-tolerance at the protein level remain unclear. Therefore, to shed further light on the molecular mechanisms of low temperature adaptation in fish, we conducted quantitative proteomics on the T. fasciatus liver using iTRAQ. Comparing the proteomic profiles of the T. fasciatus liver at 12 °C and 26 °C, a total of 3741 proteins were identified, and 160 were differentially abundant proteins (DAPs). Among the DAPs, the most significant changes were noted in proteins involved in oxidative stress (nine proteins), mitochondrial enzymes (eleven proteins) and signal transduction (thirteen proteins). The KEGG enrichment analysis indicated significant enhancement of D-arginine and D-ornithine metabolism, MAPK signalling, Wnt signalling and Gap junction pathway. Subsequently, three significantly up-regulated proteins (CIRB, HSP90 and GST) and two significantly down-regulated proteins (FLNB and A2ML1) were validated with parallel reaction monitoring (PRM) assays. Furthermore, the changes in abundance of proteins that are involved in oxidative stress, mitochondrial enzymes and signal transduction were validated at the transcriptional level with qPCR. These verification results show that the experimental data of iTRAQ are reliable. Our results not only deepen the understanding of the mechanisms underlying low-temperature tolerance in fish, but they also may contribute to the enhancement of cold tolerance during its breeding process. SIGNIFICANCE OF THE STUDY: The study focused on a comparative quantitative proteomics analysis of the T. fasciatus liver in response to low temperatures using iTRAQ, which has not yet been reported in the literatures. The results showed that the effect of low temperature on T. fasciatus is significant, including a detoxification of metabolic by-products and oxidative stress, an activation of the mitochondrial enzyme to strengthen energy metabolism, and a negative effect on signal transduction, which result in dysfunction or suboptimal performance. These low-temperature-related changes in the liver proteome of T. fasciatus can facilitate the understanding of the low temperature-related response that takes place in similar conditions in the liver and may contribute to the breeding of cold-resistant strains.

CCN3 secreted by prostaglandin E2 inhibits intimal cushion formation in the rat ductus arteriosus

The ductus arteriosus (DA), an essential fetal shunt between the pulmonary trunk and the descending aorta, changes its structure during development. Our previous studies have demonstrated that prostaglandin E₂ (PGE₂)-EP4 signaling promotes intimal cushion formation (ICF) by activating the migration of DA smooth muscle cells via the secretion of hyaluronan. We hypothesized that, in addition to hyaluronan, PGE₂ may secrete other proteins that also regulate vascular remodeling in the DA. In order to detect PGE₂ stimulation-secreted proteins, we found that CCN3 protein was increased in the culture supernatant in the presence of PGE₂ in a dose-dependent manner by nano-flow liquid chromatography coupled with tandem mass spectrometry analysis and enzyme-linked immunosorbent assay. Quantitative RT-PCR analysis revealed that PGE₂ stimulation tended to increase the expression levels of CCN3 mRNA in DA smooth muscle cells. Immunohistochemical analysis revealed that CCN3 was highly localized in the entire smooth muscle layers and the endothelium of the DA. Furthermore, exogenous CCN3 inhibited PGE₂-induced ICF in the ex vivo DA tissues. These results suggest that CCN3 is a secreted protein of the DA smooth muscle cells induced by PGE₂ to suppress ICF of the DA. The present study indicates that CCN3 could be a novel negative regulator of ICF in the DA to fine-tune the PGE₂-mediated DA remodeling.

Integrated SWATH-based and targeted-based proteomics provide insights into the retinal emmetropization process in guinea pig

Myopia is generally regarded as a failure of normal emmetropization process, however, its underlying molecular mechanisms are unclear. To investigate the retinal protein profile changes during emmetropization, we studied differential protein expressions of ocular growth in young guinea pigs at 3 and 21 days old respectively, when significant axial elongation was detected (P < 0.001, n = 10). Independent pooled retinal samples of both eyes were subjected to SWATH mass spectrometry (MS) followed by bioinformatics analysis using cloud-based platforms. A comprehensive retina SWATH ion-library consisting of 3138 (22,871) unique proteins (peptides) at 1% FDR was constructed. 40 proteins were found to be significantly up-regulated and 8 proteins down-regulated during emmetropization (≥log2 of 0.43 with ≥2 peptides matched per protein; P < 0.05). Using pathway analysis, the most significant pathway identifiable was 'phototransduction' (P = 1.412e-4). Expression patterns of 7 proteins identified in this pathway were further validated and confirmed (P < 0.05) with high-resolution Multiple Reaction Monitoring (MRM-HR) MS. Combining discovery and targeted proteomics approaches, this study for the first time comprehensively profiled protein changes in the guinea pig retina during normal emmetropization-associated eye growth. The findings of this study are also relevant to the myopia development, which is the result of failed emmetropization.

SIGNIFICANCE

Myopia is considered as a failure of emmetropization. However, the underlying biochemical mechanism of emmetropization, a visually guided process in which eye grows towards the optimal optical state of clear vision during early development, is not well understood. Retina is known as the key tissue to regulate this active eye growth. we studied eye growth of young guinea pigs and harvested their retinal tissues. A comprehensive SWATH ion library with identification of a total 3138 unique proteins were established, in which 48 proteins exhibited significant differential expressions between 3 and 21 days old. After MRM-HR confirmation, 'phototransduction' were found as the most active pathway during emmetropic eye growth. This study is the first in discovering key retinal protein players and pathways which are presumably orchestrated by biological mechanism(s) underlying emmetropization.

Effects of both cold and heat stresses on the liver of giant spiny frog Quasipaa spinosa: stress response and histological changes

Ambient temperature associated stress can affect the normal physiological functions in ectotherms. To assess the effects of cold or heat stress on amphibians, the giant spiny frogs, Quasipaa spinosa, were acclimated at 22 °C followed by being treated at 5 °C or 30 °C for 0, 3, 6, 12, 24 and 48 h, respectively. Histological alterations, apoptotic index, mitochondrial reactive oxygen species (ROS) generation, antioxidant activity indices and stress-response gene expressions in frog livers were subsequently determined. Results showed that many fat droplets appeared after 12 h of heat stress. Percentage of melanomacrophages centres significantly changed during 48 h at both stress conditions. Furthermore, the mitochondrial ROS levels were elevated in a time-dependent manner up to 6 h and 12 h in the cold and heat stress groups, respectively. The activities of superoxide dismutase, glutathione peroxidase and catalase were successively increased along the cold or heat exposure, and most of their gene expression levels showed similar changes at both stress conditions. Most tested HSP genes were sensitive to temperature exposure, and the expression profiles of most apoptosis-related genes was significantly up-regulated at 3 and 48 h under cold and heat stress, respectively. Apoptotic index at 48 h under cold stress was significantly higher than that under heat stress. Notably, lipid droplets, HSP30, HSP70 and HSP110 might be suitable bioindicators of heat stress. The results of these alterations at physiological, biochemical and molecular levels might contribute to a better understanding of the stress response of Q. spinosa and even amphibians under thermal stresses.

The Effect of rhCygb on CCl4-Induced Hepatic Fibrogenesis in Rat

This study aims to investigate whether the use of recombinant human cytoglobin (rhCygb) impact on hepatic fibrogenesis caused by CCl₄. SD (n = 150) rats were randomly divided into three groups of normal, CCl₄ model and rhCygb groups. After model establishment, rats in rhCygb groups were administered daily with rhCygb (2 mg/kg, s.c.). Histological lesions were staged according to metavir. Serum parameters including ALT, AST, HA, LN, Col III and Col IV were determined. The liver proteins were separated by 2-DE and identified. As a result, the stage of hepatic damage and liver fibrosis in rhCygb groups were significantly milder than that in CCl₄ model groups. Meanwhile, rhCygb dramatically reversed serum levels of ALT and AST, and also markedly decreased the liver fibrosis markers levels of LN, HA, Col III and Col IV. In 2-DE, 33 proteins among three groups with the same changing tendency in normal and rhCygb treated groups compared with CCl₄ model group were identified. GO analysis showed that several identified proteins involved in oxidative stress pathway. The study provides new insights and data for administration of rhCygb reversing CCl₄-induced liver fibrosis suggesting that rhCygb might be used in the treatment of liver fibrosis.

Thrombopoietin induces production of nucleated thrombocytes from liver cells in Xenopus laevis

The development of mammalian megakaryocytes (MKs) and platelets, which are thought to be absent in non-mammals, is primarily regulated by the thrombopoietin (TPO)/Mpl system. Although non-mammals possess nucleated thrombocytes instead of platelets, the features of nucleated thrombocyte progenitors remain to be clarified. Here, we provide the general features of TPO using Xenopus laevis TPO (xlTPO). Hepatic and splenic cells were cultured in liquid suspension with recombinant xlTPO. These cells differentiated into large, round, polyploid CD41-expressing cells and were classified as X. laevis MKs, comparable to mammalian MKs. The subsequent culture of MKs after removal of xlTPO produced mature, spindle-shaped thrombocytes that were activated by thrombin, thereby altering their morphology. XlTPO induced MKs in cultured hepatic cells for at least three weeks; however, this was not observed in splenic cells; this result demonstrates the origin of early haematopoietic progenitors in the liver rather than the spleen. Additionally, xlTPO enhanced viability of peripheral thrombocytes, indicating the xlTPO-Mpl pathway stimulates anti-apoptotic in peripheral thrombocytes. The development of thrombocytes from MKs via the TPO-Mpl system in X. laevis plays a crucial role in their development from MKs, comparable to mammalian thrombopoiesis. Thus, our results offer insight into the cellular evolution of platelets/MKs in vertebrates. (200/200).

Diverse of Erythropoiesis Responding to Hypoxia and Low Environmental Temperature in Vertebrates

Erythrocytes are responsible for transporting oxygen to tissue and are essential for the survival of almost all vertebrate animals. Circulating erythrocyte counts are tightly regulated and respond to erythrocyte mass and oxygen tension. Since the discovery of erythropoietin, the erythropoietic responses to environment and tissue oxygen tension have been investigated in mice and human. Moreover, it has recently become increasingly clear that various environmental stresses could induce the erythropoiesis via various modulating systems, while all vertebrates live in various environments and habitually adapt to environmental stress. Therefore, it is considered that investigations of erythropoiesis in vertebrates provide a lead to the various erythropoietic responses to environmental stress. This paper comparatively introduces the present understanding of erythropoiesis in vertebrates. Indeed, there is a wide range of variations in vertebrates' erythropoiesis. This paper also focused on erythropoietic responses to environmental stress, hypoxia, and lowered temperature in vertebrates.

Evolution of p53 transactivation specificity through the lens of a yeast-based functional assay

Co-evolution of transcription factors (TFs) with their respective cis-regulatory network enhances functional diversity in the course of evolution. We present a new approach to investigate transactivation capacity of sequence-specific TFs in evolutionary studies. Saccharomyces cerevisiae was used as an in vivo test tube and p53 proteins derived from human and five commonly used animal models were chosen as proof of concept. p53 is a highly conserved master regulator of environmental stress responses. Previous reports indicated conserved p53 DNA binding specificity in vitro, even for evolutionary distant species. We used isogenic yeast strains where p53-dependent transactivation was measured towards chromosomally integrated p53 response elements (REs). Ten REs were chosen to sample a wide range of DNA binding affinity and transactivation capacity for human p53 and proteins were expressed at two levels using an inducible expression system. We showed that the assay is amenable to study thermo-sensitivity of frog p53, and that chimeric constructs containing an ectopic transactivation domain could be rapidly developed to enhance the activity of proteins, such as fruit fly p53, that are poorly effective in engaging the yeast transcriptional machinery. Changes in the profile of relative transactivation towards the ten REs were measured for each p53 protein and compared to the profile obtained with human p53. These results, which are largely independent from relative p53 protein levels, revealed widespread evolutionary divergence of p53 transactivation specificity, even between human and mouse p53. Fruit fly and human p53 exhibited the largest discrimination among REs while zebrafish p53 was the least selective.

Cellular characterization of thrombocytes in Xenopus laevis with specific monoclonal antibodies

Platelets are produced from megakaryocytes (MKs) in the bone marrow. In contrast, most nonmammalian vertebrates have nucleated and spindle-shaped thrombocytes instead of platelets in their circulatory systems, and the presence of MKs as thrombocyte progenitors has not been verified. In developing a new animal model in adult African clawed frog (Xenopus laevis), we needed to distinguish nucleated thrombocytes and their progenitors from other blood cells, because the cellular morphology of activated thrombocytes resembles lymphocytes and other cells. We initially generated two monoclonal antibodies, T5 and T12, to X. laevis thrombocytes. Whereas T5 recognized both thrombocytes and leukocytes, T12 specifically reacted to spindle-shaped thrombocytes. The T12(+) thrombocytes displayed much higher DNA ploidy than nucleated erythrocytes, and they expressed CD41 and Fli-1. In the presence of CaCl2, adenosine diphosphate, thrombin, or various collagens, T12(+) thrombocytes exhibited aggregation. These thrombocytes were located predominantly in the hepatic sinusoids and the splenic red pulp, suggesting that both organs are the sites of thrombopoiesis. Notably, circulating thrombocytes exhibited lower DNA ploidy than hepatic thrombocytes. Intraperitoneal administration of T12 produced immune thrombocytopenia in frogs, which reached a nadir 4 days postinjection, followed by recovery, suggesting that humoral regulation maintained the number of circulating thrombocytes. Although differences between MKs and thrombocytes in X. laevis remain to be defined, our results provide further insight into MK development and thrombopoiesis in vertebrates.