Study of the gut transcriptomic response in Drosophila melanogaster with knockdown of the Gagr, domesticated gag/i> gene of errantiviruses

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Abstract

As a result of molecular domestication of the gag gene of errantiviruses, the Gagr gene was formed in the genome of Drosophila melanogaster. It has previously been shown that the Gagr gene is transcribed at the highest level in gut tissues relative to other tissues, and its transcription is most effectively induced in females in response to ammonium persulfate added to the diet. In the present work, the gut transcriptome of females with knockdown of the Gagr gene was studied in all tissues under standard conditions and under stress conditions caused by ammonium persulfate. It was revealed that in females with knockdown of the Gagr gene, the genes of animicrobial peptides controlled by the Toll and Imd signaling pathways are activated in the gut. Induction of a stress response by ammonium persulfate revealed disruption of the JAK/STAT and JNK/MAPK signaling pathways and an almost complete absence of activation of the ER-stress and UPR-stress pathways in the Gagr gene mutant. The data obtained confirm the important role of the Gagr gene in maintaining the homeostasis and the immune response.

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About the authors

M. L. Nikitina

Faculty of Biology, Lomonosov Moscow State University

Email: nefedova@mail.bio.msu.ru
Russian Federation, Moscow, 119234

P. A. Milyaeva

Faculty of Biology, Lomonosov Moscow State University

Email: nefedova@mail.bio.msu.ru
Russian Federation, Moscow, 119234

I. V. Kuzmin

Faculty of Biology, Lomonosov Moscow State University

Email: nefedova@mail.bio.msu.ru
Russian Federation, Moscow, 119234

L. N. Nefedova

Faculty of Biology, Lomonosov Moscow State University

Author for correspondence.
Email: nefedova@mail.bio.msu.ru
Russian Federation, Moscow, 119234

References

  1. Malik H.S., Henikoff S. (2005) Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster. PLoS Genet. 1(4), e44.
  2. Nefedova L.N., Kuzmin I.V., Makhnovskii P.A., Kim A.I. (2014) Domesticated retroviral GAG gene in Drosophila: new functions for an old gene. Virology. 450–451, 196.
  3. Guruharsha K.G., Rual J.-F., Zhai B., Mintseris J., Vaidya P., Vaidya N., Beekman C., Wong C., Rhee D.Y., Cenaj O., McKillip E., Shah S., Stapleton M., Wan K.H., Yu C., Parsa B., Carlson J.W., Chen X., Kapadia B., VijayRaghavan K., Gygi S.P., Celniker S.E., Obar R.A., Artavanis-Tsakonas S. (2011) A protein complex network of Drosophila melanogaster. Cell. 147, 690–703.
  4. Parua P.K., Young E.T. (2014) Binding and transcriptional regulation by 14-3-3 (Bmh) proteins requires residues outside of the canonical motif. Eukaryot. Cell. 13, 21–30.
  5. Moretti A.I.S., Laurindo F.R.M. (2017) Protein disulfide isomerases: redox connections in and out of the endoplasmic reticulum. Arch. Biochem. Biophys. 617, 106–119.
  6. Fraser C.S., Lee J.Y., Mayeur G.L., Bushell M., Doudna J.A., Hershey J.W. (2004) The j-subunit of human translation initiation factor eIF3 is required for the stable binding of eIF3 and its subcomplexes to 40 S ribosomal subunits in vitro. J. Biol. Chem. 279, 8946–8956.
  7. Majzoub K., Hafirassou M.L., Meignin C., Goto A., Marzi S., Fedorova A., Verdier Y., Vinh J., Hoffmann J.A., Martin F., Baumert T.F., Schuster C., Imler J.L. (2014) RACK1 controls IRES-mediated translation of viruses. Cell. 159, 1086–1095.
  8. Nefedova L., Gigin A., Kim A. (2022) Domesticated LTR-retrotransposon gag-related gene (Gagr) as a member of the stress response network in Drosophila. Life. 12, 364.
  9. Makhnovskii P., Balakireva Y., Nefedova L., Lavrenov A., Kuzmin I., Kim A. (2020) Domesticated gag gene of Drosophila LTR retrotransposons is involved in response to oxidative stress. Genes. 11, 396.
  10. Bunker B.D., Nellimoottil T.T., Boileau R.M., Classen A.K., Bilder D. (2015) The transcriptional response to tumorigenic polarity loss in Drosophila. Elife. 4, e03189.
  11. Dostert C., Jouanguy E., Irving P., Troxler L., Galiana-Arnoux D., Hetru C., Homann J.A., Imler J.L. (2005) The JAK/STAT signaling pathway is required but not sufficient for the antiviral response of Drosophila. Nat. Immunol. 6, 946–953.
  12. Paradkar P.N., Trinidad L., Voysey R., Duchemin J.-B., Walker P.J. (2012) Secreted Vago restricts West Nile virus infection in Culex mosquito cells by activating the JAK/STAT pathway. Proc. Natl. Acad. Sci. USA. 109, 18915–18920.
  13. Zhou Y., Zhou B., Pache L., Chang M., Khodabakhshi A.H., Tanaseichuk O., Benner C., Chanda S.K. (2019) Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10(1), 1523.
  14. Lee J.H., Cho K.S., Lee J., Yoo J., Lee J., Chung J. (2001) Diptericin-like protein: an immune response gene regulated by the anti-bacterial gene induction pathway in Drosophila. Gene. 271(2), 233–238.
  15. Agaisse H., Petersen U.M., Boutros M., Mathey-Prevot B., Perrimon N. (2003) Signaling role of hemocytes in Drosophila JAK/STAT-dependent response to septic injury. Dev. Cell. 5(3), 441–450.
  16. Biteau B., Karpac J., Hwangbo D., Jasper H. (2011) Regulation of Drosophila lifespan by JNK signaling. Exp. Gerontol. 46(5), 349.
  17. Johnson G.L., Nakamura K. (2007) The c-jun kinase/stress-activated pathway: regulation, function and role in human disease. Biochim. Bioph. Acta. 1773(8), 1341.
  18. Belozerov V.E., Lin Z.-Y., Gingras A.-C., McDermott J.C., Michael Siu K.W. (2012) High resolution protein interaction map of the Drosophila melanogaster p38 mitogen-activated protein kinases reveals limited functional redundancy. Mol. Cell. Biol. 32(18), 3695.
  19. Amoyel M., Anderson A.M., Bach E.A. (2014) JAK/STAT pathway dysregulation in tumors: a Drosophila perspective. Semin. Cell Dev. Biol. 28, 96.
  20. Kingsolver M.B., Huang Z., Hardy R.W. (2013) Insect antiviral innate immunity: pathways, effectors, and connections. J. Mol. Biol. 425(24), 4921.
  21. La Fortezza M., Schenk M., Cosolo A., Kolybaba A., Grass I., Classen A.-K. (2016) JAK/STAT signalling mediates cell survival in response to tissue stress. Development. 143(16), 2907.
  22. Ryoo H.D., Domingos P.M., Kang M.-J., Steller H. (2007) Unfolded protein response in a Drosophila model for retinal degeneration. EMBO J. 26(1), 242.
  23. Ryoo H.D. (2015) Drosophila as a model for unfolded protein response research. BMB Rep. 48(8), 445.
  24. Hollien J., Weissman J.S. (2006) Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response. Science. 313(5783), 104.
  25. Hewes R.S., Schaefer A.M., Taghert P.H. (2000) The cryptocephal gene (ATF4) encodes multiple basic-leucine zipper proteins controlling molting and metamorphosis in Drosophila. Genetics. 155(4), 1711.
  26. Brown B., Finnegan S.M., Roach D., Vasudevan D., Ryoo H.D. (2021) The transcription factor Xrp1 is required for PERK-mediated antioxidant gene induction in Drosophila. eLife. 10, e74047.
  27. He Y., Chen Y., Song W., Zhu L., Dong Z., Ow D.W. (2017) A Pap1–Oxs1 signaling pathway for disulfide stress in Schizosaccharomyces pombe. Nucl. Acids Res. 45, 106–114.
  28. Kudo N., Taoka H., Toda T., Horinouchi S. (1999) A novel nuclear export signal sensitive to oxidative stress in the fission yeast transcription factor Pap1. J. Biol. Chem. 274, 15151–15158.
  29. Li S., Wang L., Fu B., Berman M.A., Diallo A., Dorf M.E. (2014) TRIM65 regulates microRNA activity by ubiquitination of TNRC6. Proc. Natl. Acad. Sci. USA. 111, 6970–6975.
  30. Malinová A., Cvačková Z., Matějů D., Hořejší Z., Abéza C., Vandermoere F., Bertrand E., Staněk D., Verheggen C. (2017) Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. J. Cell Biol. 216, 1579–1596.
  31. Kırlı K., Karaca S., Dehne H.J., Samwer M., Pan K.T., Lenz C., Urlaub H., Görlich D. (2015) A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. Elife. 4, e11466.
  32. Telkoparan P., Erkek S., Yaman E., Alotaibi H., Bayık D., Tazebay U.H. (2013) Coiled-coil domain containing protein 124 is a novel centrosome and midbody protein that interacts with the Ras-guanine nucleotide exchange factor 1B and is involved in cytokinesis. PLoS One. 8, e69289.
  33. Castello A., Fischer B., Eichelbaum K., Horos R., Beckmann B.M., Strein C., Davey N.E., Humphreys D.T., Preiss T., Steinmetz L.M., Krijgsveld J., Hentze M.W. (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell. 149, 1393–1406.
  34. Wells J.N., Buschauer R., Mackens-Kiani T., Best K., Kratzat H., Berninghausen O., Becker T., Gilbert W., Cheng J., Beckmann R. (2020) Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. PLoS Biol. 18(7), e3000780.

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9. Fig. 1. Comparative analysis of intestinal transcriptomes of Gagr knockdown and control females. a – Heat map and cluster analysis of intestinal transcriptomes of Gagr knockdown and control females cultured under standard conditions and on APS-containing medium. b – Enrichment of functional categories of genes with differential expression (|LFC| > 2) in the intestine of Gagr knockdown females relative to the control line. The abscissa scale shows the negative logarithm of the P-value for a given category. c – Enrichment of functional categories of genes with increased and decreased transcription during stress response (|LFC| > 2) in control and Gagr knockdown females. (g) Venn diagrams showing the number of common genes whose transcription was altered by stress response in control (C) and Gagr knockdown (Gagr-RNAi) females and their enrichment in functional categories.

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10. Fig. 2. Enrichment of functional categories of genes with increased transcription (LFC > 2) in the intestine of control females and unchanged or decreased transcription in the intestine of Gagr knockdown females (LFC < 0.5). The cluster network of functional categories of genes constructed in the Metascape program is shown below the diagram (explanations in the text).

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11. Fig. 3. Transcriptional response of the genes of the JNK/MAPK, JAK/STAT, and ER stress signaling pathways in response to ammonium persulfate in the intestines of control females (a) and females with Gagr knockdown (b). To construct the signaling pathway diagrams, data from [20] and [23] were used. Genes whose transcription increased more than 2-fold are shown in red. Genes whose expression increased 1.5–2-fold are highlighted in pink. The LFC value is given in brackets near the genes, kinases are highlighted in bold; xbp1s is the spliced ​​form of xbp1. *TotA – expression of this gene in individuals with knockdown is lower than in the control, but is induced during the stress response; **hid – expression of this gene in individuals with Gagr knockdown is higher than in the control, and is not induced during the stress response.

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