Environmental acclimatization of the carp modulates the transcription of beta-actin

Evaluation of reference genes for reverse transcription-quantitative PCR assays in organs of zebrafish exposed to glyphosate-based herbicide, Roundup

Roundup is a glyphosate-based herbicide (GBH) widely used in agriculture and may cause toxic effects in non-target organisms. Model organisms, as zebrafish, and analysis of gene expression by reverse transcription-quantitative PCR (RT-qPCR) could be used to better understand the Roundup toxicity. A prerequisite for RT-qPCR is the availability of appropriate reference genes; however, they have not been described for Roundup-exposed fish. The aim of this study was to evaluate the expression stability of six reference genes (rpl8, β-act, gapdh, b2m, ef1α, hprt1) and one expressed repetitive element (hatn10) in organs of males (brain, gill, testis) and females (ovary) of zebrafish exposed to Roundup WG at three concentrations (0.065, 0.65 and 6.5 mg N-(phosphonomethyl) glycine/l) for 7 days. Genes were ranked by geNorm, NormFinder, BestKeeper, Delta C t and RefFinder, and their best combinations were determined by geNorm and NormFinder programs. The two most stable ranked genes were specific to each organ: gill (β-act; rpl8); brain (rpl8; β-act); testis (ef1α; gapdh); and ovary (rpl8; hprt1). The cat transcript level was used to evaluate the effect of normalization with these reference genes. These are the first suitable reference genes described for the analysis of gene expression in organs of Roundup-exposed zebrafish, and will allow investigations of the molecular mechanisms of Roundup toxicity.

Next-generation transcriptome profiling reveals insights into genetic factors contributing to growth differences and temperature adaptation in Australian populations of barramundi (Lates calcarifer)

Identification of genetically-regulated adaptation in fish is a precursor to understanding how populations will respond to future climate induced stressors like temperature. Australian populations of barramundi (Lates calcarifer) show strong evidence of local adaptation to temperature. However, the phenotypic consequences of this adaptation are unknown and the genetic mechanisms underlying this response are poorly understood. In the current study, two populations of barramundi from temperature extremes of the species Australian distribution were communally reared at cool (22°C), control (28°C) and hot (36°C) water temperatures for 3.5months. Southern populations of barramundi originating from a cooler environment grew significantly faster at 22°C than northern populations of warm adapted barramundi. However, no difference in population growth was present at either 28°C or 36°C. The underlying transcriptome profile of barramundi was examined via Illumina mRNA deep sequencing to determine the major contributing gene categories giving rise to phenotypic differences in barramundi population growth. Gene ontology (GO) analysis revealed enrichment in categories relating to the regulation of peptidase activity as well as microtubule, cytoplasmic and cellular metabolic based processes. Further analysis of the GO category "microtubule based process" with associated genes from the "response to stress" category revealed an apparent re-organization of cytoskeletal elements in response to an induced cold stress in northern barramundi reared at 22°C, when compared with northern barramundi reared at 36°C. Between southern barramundi and northern barramundi reared at 36°C, an analysis of the "endopeptidase inhibitor activity" GO category in conjunction with stress genes indicated a suppression of the complement system in southern barramundi along with an increase in the cellular stress response. The results of the present study show that southern populations of barramundi exhibit underlying molecular adaptation to cooler water temperatures, but still retain a tolerance for warm water temperatures. Furthermore, GO profiling has revealed groups of genes that underlie population differences in temperature tolerance as a means to prioritize the analysis of differential gene expression in studies of local adaptation in the future.

From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

Background

Our understanding of the importance of transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and the consistency of transcriptional stress responses to different types of environmental stress. In this study, we used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures.

Results

We identified a series of gene functions that were involved in all stress responses examined here, suggesting some common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes; the responses of individual genes varied greatly across different stress types. In response to heat exposure over five days, a total of 324 gene loci were differentially expressed. Many heat-responsive genes had functions associated with protein turnover, metabolism, and the response to oxidative stress. We were also able to identify groups of co-regulated genes, the genes within which shared similar functions.

Conclusion

This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. We have shown that different types of environmental stress induce expression changes in genes with similar gene functions, but that the responses of individual genes vary between stress types. The functions of heat-responsive genes suggest that prolonged heat exposure leads to oxidative stress and protein damage, a challenge of the immune system, and the re-allocation of energy sources. This study hence offers insight into the effects of environmental stress on biological function and sheds light on the expected sensitivity of coral reef fishes to elevated temperatures in the future.

Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real-time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.

Gene structure and seasonal expression of carp fish prolactin short receptor isoforms

The complex adaptive mechanisms that eurythermal fish have evolved in response to the seasonal changes of the environment include the transduction of the physical parameter variations into neuroendocrine signals. Studies in carp (Cyprinus carpio) have indicated that prolactin (PRL) and growth hormone (GH) expression is associated with acclimatization, suggesting that the pituitary gland is a relevant physiological node in this adaptive process. Also, the distinctive pattern of expression that carp prolactin receptor (PRLr) protein depicts upon seasonal acclimatization supports the hypothesis that PRL and its receptor clearly are involved in the new homeostatic stage that the eurythermal fish needs to survive during the cyclical changes of its habitat. Here, we characterize the first prolactin receptor gene in a teleost and show that its expression is not associated with alternative promoters, unlike in humans and rodents. Using the regulatory region to direct the transcription of green fluorescent protein (GFP) in zebrafish embryos, we mapped the appearance of this hormone receptor during fish development. This is the first report identifying a fish prolactin receptor gene expressing transcript isoforms encoding for short forms of the protein (45 kDa). These have been found in osmoregulatory tissues of the carp and are regulated in connection with the seasonal acclimatization of the fish.

Expression profiling and validation of reference gene candidates in immune relevant tissues and cells from Atlantic salmon (Salmo salar L.)

The expression levels of three commonly used housekeeping genes, EF1-alpha, RPS20 and Beta-Actin, were examined in seven different tissues and leucocytes from non-stimulated Atlantic salmon (Salmo salar L.). The tissues analysed by quantitative real-time PCR were gill, liver, intestine, muscle, spleen, head kidney leucocytes (HKL) and peripheral blood leucocytes (PBL). The experiments were performed to investigate the transcriptional stability within and between tissues and leucocytes and between individuals. For all tissues and leucocytes, an appropriate reference gene was identified except for muscle tissue. HKL were used as a calibrator and the expression of EF1-alpha varied maximally 2.5-fold in five out of the six tissues and leucocytes investigated relative to the expression of 18S rRNA. The RPS20 gene was more intermediate and varied at least by a factor of two and maximally by a 20-fold factor. Beta-Actin was generally the most regulated gene showing high variations for gill (5.8x) and spleen tissue (10.3x) relative to the calibrator. A suitable reference gene for muscle tissue was not found since the expression varied between 8.3- and 25-fold for the three genes compared to the calibrator. By comparing the expression results of the non-stimulated tissues and leucocytes using the Normfinder programme, it was further shown that EF1-alpha was the most stably expressed gene both between individuals and the different tissues/leucocytes. Stimulation with lipopolysaccharide (LPS) of TO cells and HKL from Atlantic salmon was additionally performed to reveal whether an immune stimulating agent would change the expression level of EF1-alpha, RPS20 and Beta-Actin. LPS stimulation of cells revealed that RPS20 and EF1-alpha were least regulated by the LPS treatment in the TO cells relative to 18S rRNA, but in HKL, Beta-Actin was the most appropriate gene. However, the variations were overall maximally two-fold in LPS-stimulated TO cells and HKL, which make all three genes suitable as reference genes in this case. A further experiment showed that no RT- and/or PCR inhibitors were present in the non-stimulated tissues and cells, indicating true transcriptional differences.

Steady-state effects of temperature acclimation on the transcriptome of the rainbow trout heart

Cold-acclimated (CA) phenotype of trout heart was induced by 4-wk acclimation at 4°C and was characterized by 32.7% increase in relative heart mass and 49.8% increase in ventricular myocyte size compared with warm-acclimated (WA; 18°C) fish ( P < 0.001). Effect of temperature acclimation on transcriptome of the rainbow trout heart was examined using species-specific microarray chips containing 1,380 genes. After 4 wk of temperature acclimation, 8.8% (122) of the genes were differently expressed in CA and WA hearts, and most of them (82%) were upregulated in the cold ( P < 0.01). Transcripts of genes engaged in protein synthesis and intermediary metabolism were most strongly upregulated, whereas genes contributing to the connective tissue matrix were clearly repressed. Extensive upregulation of the genes coding for ribosomal proteins and translation elongation and initiation factors suggest that the protein synthesis machinery of the trout heart is enhanced in the cold and is an essential part of the compensatory mechanism causing and maintaining the hypertrophy of cardiac myocytes. The prominent depression of collagen genes may be indicative of a reduced contribution of extracellular matrix to the remodeling of the CA fish heart. Temperature-related changes in transcripts of metabolic enzymes suggest that at mRNA level, glycolytic energy production from carbohydrates is compensated in the heart of CA rainbow trout, while metabolic compensation is absent in mitochondria. In addition, the analysis revealed three candidate genes: muscle LIM protein, atrial natriuretic peptide B, and myosin light chain 2, which might be central for induction and maintenance of the hypertrophic phenotype of the CA trout heart. These findings indicate that extensive modification of gene expression is needed to maintain the temperature-specific phenotype of the fish heart.

Seasonal modulation of growth hormone mRNA and protein levels in carp pituitary: evidence for two expressed genes

Adaptation of eurythermal fish to naturally varying environmental conditions involves modulation of expressions of various factors in the hypothalamo-hypophyseal axis. Here we used three complementary approaches to assess the seasonal variation of growth hormone (GH) protein and mRNA levels in pituitary glands of acclimatized carp fish. First, a polyclonal antibody raised against an oligopeptide derived from the carp GH sequence was used for immunohistochemistry; second, oligonucleotides specific for GH transcripts were used for in situ hybridization. Specific immunodetection of GH coincides with visualization of GH mRNA in the proximal pars distalis, the specific location of somatotroph cells in carp pituitary gland. Finally, competitive RT-PCR analyses confirmed that GH expression exhibits seasonal cyclical reprogramming with higher levels in summer- than in winter-adapted fish. The expression pattern suggests an important role for GH in the molecular mechanisms underlying the acclimatization process. In parallel, amplification of sequences from the fourth intron and adjacent sites from exons IV and V demonstrates the existence of a new GH gene previously undescribed. The detection of transcripts corresponding to each gene suggests that both GH gene copies are active in the duplicated carp genome and that they are similarly affected by seasonal adaptation.

Effects of endocrine disrupting chemicals on the expression of CYP19 genes in zebrafish (Danio rerio) juveniles

Cytochrome P450 aromatase (CYP19) is the key steroidogenic enzyme responsible for conversion of androgens to estrogens which play a critical role in developmental sex differentiation and adult reproductive cycles in vertebrates. To evaluate the potential roles of endocrine disrupting chemicals (EDC) on reproductive physiology of fish, the influence of multiple classes of EDC on the transcript abundance of two CYP19 isoforms, CYP19A1 and A2, were investigated in zebrafish juveniles. The pharmaceutical, clofibrate, and the pesticide, atrazine, did not influence the expression of either CYP19 gene. Estrogenic compounds, nonylphenol (NP) and a pharmaceutical estrogen, ethinylestradiol (EE), strongly enhanced the expression of CYP19A2 gene in dose-dependent manner. Exposure to benzo[a]pyrene (BaP) significantly increased CYP19A2 transcript abundance. Furthermore, BaP when co-treated with EE partially suppressed EE-induced upregulation of CYP19A2. In contrast, the expression of CYP19A1 was basically resistant to EDC treatment although EE at high concentration (1-100 nM) downregulated its expression. These findings suggest that multiple classes of EDC may potentially perturb developmental and reproductive physiology in fish through differential transcriptional modulation of the CYP19 genes with the most evident disruption in neural tissue.

Temperature-dependent enhancement of cell proliferation and mRNA expression for type I collagen and HSP70 in primary cultured goldfish cells

Goldfish (Carasius auratus) primary culture cells derived from caudal fin were incubated over a temperature range of 20-35 degrees C. The population doubling time of cells cultured at 20, 25, 30 and 35 degrees C were 34, 29, 17 and 14 h, respectively. Interestingly, cDNA-representational difference analysis revealed type I collagen alpha chain (colalpha(I)) as a candidate for a warm temperature-specific gene. mRNA levels of colalpha(I) increased with an increase of incubation temperature and days of culture. Furthermore, the cell growth rate and colalpha(I) mRNA levels were rapidly changed following temperature shifts. To examine the effects of culture temperature shift on the cellular physiological states, mRNA levels of HSP70 were additionally investigated. HSP70 mRNA levels in the cells cultured at 30 and 35 degrees C were again 2-3 times higher than those at 20 and 25 degrees C. When the culture temperature was shifted from 20 to 35 degrees C, HSP70 mRNA levels were rapidly increased within 1 h. Subsequently, mRNA levels of the 35 degrees C-treated cells decreased, but remained doubled compared with those of the 20 degrees C-treated cells, even 4 h following the temperature shift. When the culture temperature was lowered from 35 to 20 degrees C, HSP70 mRNA levels decreased to about 70% of the original levels in 4 h. These results indicate that goldfish cells cultured at different temperatures easily develop temperature-associated steady physiological states within 4 h of temperature shifts.

Seasonal environmental changes modulate the prolactin receptor expression in an eurythermal fish

Eurythermal fish have evolved compensatory responses to the cyclical seasonal changes of the environment. The complex adaptive mechanisms include the transduction of the physical parameters variations into molecular signals. Studies in carp have indicated that prolactin and growth hormone expression is associated with acclimatization, suggesting that the pituitary gland is a relevant physiological node in the generation of the homeostatic rearrangement that occurs in this adaptive process. Here, we report the cloning and characterization of a full-length carp prolactin receptor cDNA, which codes for the long form of the protein resembling that found in mammalian prolactin receptors. We identified up to three receptor transcript isoforms in different tissues of the teleost and assessed cell- and temporal-specific transcription and protein expression in carp undergoing seasonal acclimatization. The distinctive pattern of expression that carp prolactin receptor (cPRLr) depicts upon seasonal acclimatization supports the hypothesis that prolactin and its receptor are clearly involved in the new homeostatic stage that the eurythermal fish needs to survive during the cyclical changes of its habitat.

Hypophyseal gene expression profiles of FSH-beta, LH-beta, and glycoprotein hormone-alpha subunits in Ictalurus punctatus throughout a reproductive cycle

A determination of the seasonal changes in the expression of the genes encoding the subunits of gonadotropic hormones is an important first step in the understanding of the molecular control of the onset of puberty and the reproductive cycle in fish. In this study, the abundance of transcripts encoding the glycoprotein hormone alpha (GpH-alpha), follicle-stimulating hormone beta (FSH-beta), and luteinizing hormone beta (LH-beta) subunits in pituitaries of female channel catfish were systematically tracked throughout an annual reproductive cycle. All three genes showed a concurrent elevation coinciding with the onset of ovarian recrudescence but then each showed a second elevation at different times of the ovarian cycle. In addition to the initial peak at recrudescence, the expression of FSH-beta and GpH-alpha gene peaked again during mid- and late-vitellogenic growth, respectively. The LH-beta gene expression remained low during the phases of regression and vitellogenic growth but was moderately elevated (7-fold) at the onset of ovarian recrudescence and dramatically elevated (36-fold) just prior to spawning (June-July) when the FSH-beta levels were at their lowest. The expression patterns of FSH-beta and LH-beta are remarkably similar to the ovarian expression of their respective receptors.