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Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun 2020; 11:781. [PMID: 32034123 PMCID: PMC7005711 DOI: 10.1038/s41467-020-14500-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/20/2019] [Indexed: 11/14/2022] Open
Abstract
Recent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Here, we systematically characterize how these de novo emerging coding sequences impact fitness in budding yeast. Disruption of emerging sequences is generally inconsequential for fitness in the laboratory and in natural populations. Overexpression of emerging sequences, however, is enriched in adaptive fitness effects compared to overexpression of established genes. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich non-genic regions and subsequently accumulate changes molded by natural selection. There is increasing evidence that protein-coding genes can emerge de novo from noncoding genomic regions. Vakirlis et al. propose that sequences encoding transmembrane polypeptides can emerge de novo in thymine-rich genomic regions and provide organisms with fitness benefits.
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Affiliation(s)
- Nikolaos Vakirlis
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, 2, Ireland
| | - Omer Acar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Brian Hsu
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - Nelson Castilho Coelho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - S Branden Van Oss
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Kate Medetgul-Ernar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - Ray W Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States
| | - Cameron P Hines
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - John Iannotta
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Saurin Bipin Parikh
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, 2, Ireland
| | - Carlos J Camacho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Allyson F O'Donnell
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States. .,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States.
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States.
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States. .,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.
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Pelletier L, Rebouissou S, Paris A, Rathahao-Paris E, Perdu E, Bioulac-Sage P, Imbeaud S, Zucman-Rossi J. Loss of hepatocyte nuclear factor 1alpha function in human hepatocellular adenomas leads to aberrant activation of signaling pathways involved in tumorigenesis. Hepatology 2010; 51:557-66. [PMID: 20041408 DOI: 10.1002/hep.23362] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
UNLABELLED Hepatocellular adenomas (HCAs) are benign liver tumors that usually develop in women who are taking oral contraceptives. Among these tumors, biallelic inactivating mutations of the hepatocyte nuclear factor 1alpha (HNF1A) transcription factor have been frequently identified and in rare cases of hepatocellular carcinomas developed in noncirrhotic liver. Because HNF1A meets the genetic criteria of a tumor suppressor gene, we aimed to elucidate the tumorigenic mechanisms related to HNF1alpha inactivation in hepatocytes. We searched for signaling pathways aberrantly activated in human HNF1A-mutated HCA (H-HCA) using a genome-wide transcriptome analysis comparing five H-HCA with four normal livers. We validated the main pathways by quantitative reverse transcription polymerase chain reaction (RT-PCR) and western blotting in a large series of samples. Then, we assessed the role of HNF1alpha in the observed deregulations in hepatocellular cell models (HepG2 and Hep3B) by silencing its endogenous expression using small interfering RNA. Along with the previously described induction of glycolysis and lipogenesis, H-HCA also displayed overexpression of several genes encoding growth factor receptors, components of the translation machinery, cell cycle, and angiogenesis regulators, with, in particular, activation of the mammalian target of rapamycin (mTOR) pathway. Moreover, estradiol detoxification activities were shut down, suggesting a hypersensitivity of H-HCA to estrogenic stimulation. In the cell model, inhibition of HNF1alpha recapitulated most of these identified transcriptional deregulations, demonstrating that they were related to HNF1alpha inhibition. CONCLUSION H-HCA showed a combination of alterations related to HNF1alpha inactivation that may cooperate to promote tumor development. Interestingly, mTOR appears as a potential new attractive therapeutic target for treatment of this group of HCAs.
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Affiliation(s)
- Laura Pelletier
- Institut National de la Sante et de la Recherche Medicale, U674, Génomique fonctionnelle des tumeurs solides, Paris, France
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Abstract
Steroidal oestrogens have been isolated from marine and terrestrial animals representative of all major classes of vertebrates including fish, amphibians, reptiles, birds and mammals. In general, oestrogens are responsible for most features characteristic of the female sex of a species, such as metabolic, behavioural and morphological changes during the stages of reproduction; they also support several processes in males. The evolution of the hormonal system always involves both the ligand and its sites of interaction. In the case of oestrogens, the steroid producing enzymes, mainly the aromatase complex, and the oestrogen receptor belong together within their co-evolution. The finding of oestrogenic steroids, the more recent identification of aromatase and receptor genes and their expression fit together, thereby confirming the importance for all vertebrates. Within the present paper, the evolution of the physiological functions of oestrogens from oviparous vertebrates to Eutherian mammals, oestrogen biosynthesis, metabolization and signalling pathways will be reviewed in detail.
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Affiliation(s)
- Iris G Lange
- Institute of Physiology, Centre of Milk and Food Research Weihenstephan, Technical University Munich, Weihenstephaner Berg 3, D-85354 Freising, Germany.
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Vihma V, Adlercreutz H, Tiitinen A, Kiuru P, Wähälä K, Tikkanen MJ. Quantitative Determination of Estradiol Fatty Acid Esters in Human Pregnancy Serum and Ovarian Follicular Fluid. Clin Chem 2001. [DOI: 10.1093/clinchem/47.7.1256] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractBackground: Lipophilic estradiol derivatives carried by lipoprotein particles in blood may mediate antioxidant or endocrine effects. We developed a new quantitative method to determine the concentration of circulating lipophilic estradiol fatty acid esters in human early- and late-pregnancy serum and in ovarian follicular fluid.Methods: After extraction from serum or follicular fluid, estradiol fatty acid esters were separated from nonesterified estradiol by Sephadex LH-20 column chromatography. The estradiol ester fraction was hydrolyzed by saponification and further purified by several chromatographic steps. The hydrolyzed estradiol esters were measured by time-resolved fluoroimmunoassay.Results: The average estradiol fatty acid ester concentration in serum increased 10-fold during pregnancy, from 40.4 pmol/L (expressed as pmol/L estradiol; range, 25.0–64.2 pmol/L) in early pregnancy (n = 8) to 404 pmol/L (196–731 pmol/L) in late pregnancy (n = 10). The ratio of estradiol ester to nonesterified estradiol remained relatively constant during pregnancy, at 0.4–0.6%. In 10 follicular fluid samples, the mean estradiol ester concentration was 106 nmol/L (56.9–262 nmol/L). Compared with serum, a greater proportion of estradiol in follicular fluid (3.0–10%) was in the esterified form.Conclusion: The new method provides a means to measure circulating estradiol fatty acid ester concentrations in human pregnancy serum.
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Affiliation(s)
| | - Herman Adlercreutz
- Department of Clinical Chemistry, Folkhälsan Research Center, PB 60, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Aila Tiitinen
- Obstetrics and Gynecology, PB 140, Helsinki University Central Hospital, 00290 Helsinki, Finland
| | - Paula Kiuru
- Department of Organic Chemistry, PB 55, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Kristiina Wähälä
- Department of Organic Chemistry, PB 55, University of Helsinki, FIN-00014 Helsinki, Finland
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Young AJ, Barker KL. Effect of estradiol and progesterone on long chain fatty acyl-coenzyme A levels in the rat uterus. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1092:211-7. [PMID: 2018788 DOI: 10.1016/0167-4889(91)90159-u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fatty acyl-CoAs are potential in vivo inactivators of glucose-6-phosphate dehydrogenase (G6PD). Ovariectomized mature rats (n = 74) were given 5 micrograms of estradiol intravenously, then killed 0, 24, 36, 48 and 72 h later. Control levels of myristoyl-, palmitoyl-, stearoyl-, arachidonoyl-, oleoyl- and linoleoyl-CoA were 0.6, 3.2, 4.7, 3.4, 2.4 and 3.0 micrograms/uterus and were increased 39, 110, 146, 100, 84 and 69% at 36-48 h, respectively. Levels of fatty acyl-CoAs in the rat uterus become elevated 36 h after estradiol treatment. At the same time G6PD changes from a stable enzyme to one that is irreversibly inactivated, possibly due to being rapidly degraded. Progesterone (2 mg subcutaneously every 12 h, n = 30), administered beginning at either 24 or 36 h after estradiol treatment, had no effect on estradiol-induced changes in myristoyl-, palmitoyl-, or stearoyl-CoA. Compared to the groups of rats treated with estradiol alone, animals treated with combinations of estradiol and progesterone exhibited higher levels of arachidonoyl-CoA after 48 h, and oleoyl-CoA and linoleoyl-CoA were greater after 72 h. Progesterone increased the estradiol-induced levels of unsaturated fatty acyl-CoAs suggesting that progesterone may induce uterine fatty acid desaturase activity and/or uptake of dietary fatty acids. Addition of fatty acyl-CoAs, at concentrations seen in vivo at 36-48 h after estradiol, to purified G6PD, causes irreversible G6PD inactivation.
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Affiliation(s)
- A J Young
- Department of Biochemistry and Molecular Biology, Texas Tech Health Sciences Center, Lubbock 79430
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Abstract
Recent studies suggest that, estriol, like estradiol, is biosynthetically esterified with fatty acids. We have synthesized the stearate estriol, at C-16 alpha, C-17 beta and the diester, C-16 alpha,17 beta and tested these D-ring esters for their estrogenic action both in vivo and in vitro, comparing them to estradiol, estriol and estradiol-17-stearate. None of the estriol esters bind to the estrogen receptor. They are only weakly estrogenic in a microtiter plate estrogen bioassay: stimulation of alkaline phosphatase in the Ishikawa endometrial cells. However, both estriol monoesters are extremely potent estrogens when injected subcutaneously (in aqueous alcohol) into ovariectomized mice. Compared to the free steroids, they produced a dramatically increased uterine weight with a greatly prolonged duration of stimulation. The 16 alpha,17 beta-diester also induced a protracted uterotrophic response, but the stimulation of uterine weight was comparatively low. Since the esters of estradiol and estriol do not bind to the estrogen receptor, their estrogenic signal must be generated through the action of esterase enzymes. These naturally occurring esters have the potential of being extremely useful pharmacological agents for long-lived estrogenic stimulation.
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Affiliation(s)
- J E Zielinski
- Department of Obstetrics and Gynecology, Yale University School of Medicine, New Haven, CT 06510
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Abstract
Several years ago we discovered an unexpected family of steroidal metabolites, steroidal fatty acid esters. We found that fatty acid esters of 5-ene-3 beta-hydroxysteroids, pregnenolone and dehydroisoandrosterone are present in the adrenal. Subsequently, others have shown the existence of these non-polar 5-ene-3 beta-hydroxysteroidal esters in blood, brain and ovaries. Currently, almost every family of steroid hormone is known to occur in esterified form. We have studied the esters of the estrogens and glucocorticoids in some detail, and have found that these two steroidal families are esterified by separate enzymes. In a biosynthetic experiment performed simultaneously with estradiol and corticosterone, we established that the fatty acid composition of the steroidal esters is quite different. The corticoid is composed predominantly of one fatty acid, oleate, while the estradiol esters are extremely heterogeneous. Our studies have demonstrated that the estrogens are extremely long-lived hormones, that they are protected by the fatty acid from metabolism. They are extremely potent estrogens, with prolonged activity. Esterification appears to be the only form of metabolism that does not deactivate the biological effects of estradiol. We have demonstrated the biosynthesis of fatty acid esters of estriol, monoesters at both C-16 alpha and C-17 beta. They too are very potent estrogens. These fatty acid esters of the estrogens are the endogenous analogs of estrogen esters, like benzoate, cypionate, etc., which have been used for decades, pharmacologically because of their prolonged therapeutic potency. We have found that the estradiol esters are located predominantly in hydrophobic tissues, such as fat. Sequestered in these tissues, they are an obvious reservoir of estrogenic reserve, requiring only an esterase for activation. To the contrary the biological activity of the fatty acid esters of the glucocorticoid, corticosterone, is not different from that of its free parent steroid. We have shown that the rapid kinetics of its induction of gluconeogenic responses is caused by its labile C-21 ester which is rapidly hydrolyzed by esterase enzymes. While it appears that the physiological role of the estrogen esters may be related to their long-lived hormonal activity, the role of the other families of steroidal esters is not yet apparent. They, and perhaps the estrogen esters as well, must serve other purposes. Indeed they may serve important biological functions beyond those which we ordinarily associate with steroid hormones.
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Affiliation(s)
- R B Hochberg
- Department of Obstetrics and Gynecology, Yale University School of Medicine, New Haven, CT 06510
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