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. 2022 Nov 15;2022:10.17912/micropub.biology.000679. doi: 10.17912/micropub.biology.000679

Drosophila simulans – Ilp2

Leon F Laskowski 1, Cole A  Kiser 2, Robyn  Huber 3, Sean Kusche 4, Andrew M Arsham 3, Thomas C  Giarla 4, Chinmay P Rele 2,§
Reviewed by: GEP Review Panel
PMCID: PMC9709637  PMID: 36468154

Figure 1.

Figure 1.

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(A) Synteny comparison of the genomic neighborhoods for Ilp2 in Drosophila melanogaster and D. simulans . Thin underlying arrows indicate the DNA strand within which the target gene– Ilp2 –is located in D. melanogaster (top) and D. simulans (bottom). Thin arrow(s) pointing to the right indicate(s) that Ilp2 is on the positive (+) strand in D. simulans and D.melanogaster . The wide gene arrows pointing in the same direction as Ilp2 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Ilp2 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. simulans indicate orthology to the corresponding gene in D. melanogaster . Gene symbols given in the D. simulans gene arrows indicate the orthologous gene in D. melanogaster , while the locus identifiers are specific to D. simulans . (B) Gene Model in GEP UCSC Track Data Hub (Raney et al ., 2014). The coding-regions of Ilp2 in D. simulans are displayed in the User Supplied Track (black); coding exons are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. simulans ), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster ), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. simulans ), and Splice Junctions Predicted by regtools using D. simulans RNA-Seq (Graveley et al. , 2011; SRP006203). Splice junctions shown have a read-depth of 50-99 supporting reads in green. (C) Dot Plot of Ilp2-PA in D. melanogaster ( x -axis) vs. the orthologous peptide in D. simulans ( y -axis). Amino acid number is indicated along the left and bottom; coding-exon number is indicated along the top and right, and exons are also highlighted with alternating colors. The boxes highlighted in red and yellow (Box Y; Box Z) indicate lack of sequence similarity between amino acids.

Description

Introduction The Insulin Signaling Pathway is a highly conserved signaling pathway in animals, and is central to nutrient uptake (Hietakangas and Cohen 2009, Grewal 2009). Ilp2 (aka dilp2, Dilp 2, DILP, dilp-2, Ilp-2 ), a member of the Insulin Signaling Pathway, mediates growth by acting as a ligand for the insulin receptor and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al. , 2001, Park et al. , 2014). Ilp2 plays a role in regulating body size by increasing cell size and cell number of individual organs (Ren et al. , 2017). Evolutionary studies showed that loss of Ilp2 increased lifespan, and changes in Ilp2 expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al. , 2010). In the absence of Ilp2 , over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al. , 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al. , 2010).

We propose a gene model for the D. simulans ortholog of the D. melanogaster Insulin-like peptide 2 (Ilp2) gene. The genomic region of the ortholog corresponds to the uncharacterized protein LOC6737491 (RefSeq accession XP_002084327.1) in the ASM75419v3 Genome Assembly of D. simulans (GenBank Accession: GCA_000754195.3 - Graveley et al. , 2011; SRP006203). This model is based on RNA-Seq data from D. simulans (Graveley et al. , 2011; SRP006203) and Ilp2 in D. melanogaster using FlyBase release FB2022_04 (GCA_000001215.4; Larkin et al. , 2021). D. simulans is part of the melanogaster species group within the subgenus Sophophora of the genus Drosophila (Sturtevant, 1939; Bock and Wheeler, 1972). It was first described by Sturtevant (1919). D. simulans is a sibling species to D. melanogaster , thus extensively studied in the context of speciation genetics and evolutionary ecology (Powell, 1990). Historically, D. simulans was a tropical species native to sub-Saharan Africa (Lemeunier et al ., 1986) where figs served as a primary host (Lachaise and Tsacas, 1983). However, D. simulans ’s range has expanded world-wide within the last century as a human commensal using a broad range of rotting fruits as breeding sites (https://www.taxodros.uzh.ch). The Genomics Education Partnership maintains a mirror of the UCSC Genome Browser (Kent WJ et al. , 2002; Gonzalez et al. , 2021), which is available at https://gander.wustl.edu .

Synteny

The target gene, Ilp2, occurs on chromosome 3L in D. melanogaster and is flanked upstream by Z band alternatively spliced PDZ-motif protein 67 (Zasp67), Insulin-like peptide (Ilp1) and CG32052, which nests Ilp2, Ilp3 and Ilp4 . Ilp2 is flanked downstream by Insulin-like peptide 3 (Ilp3) , Insulin-like peptide 4 (Ilp4), Insulin-like peptide 5 (Ilp5) (nested within CG43897 ), and Inhibitor-2 (I-2) . The tblastn search of D. melanogaster Ilp2-PA (query) against the D. simulans (GenBank Accession: GCA_000754195.3) Genome Assembly (database) placed the putative ortholog of Ilp2 within scaffold chromosome 3L (CM002912.1) at locus LOC6737491 (XP_002084327.1)— with an E-value of 5e-97 and a percent identity of 97.81%. Furthermore, the putative ortholog is flanked upstream by LOC6737489 (XP_016031285.1), LOC6737490 (XP_002084326.1) and LOC6737494 (XP_016031282.1), which correspond to Zasp67 , Ilp1 and CG32052 in D. melanogaster (E-value: 0.0, 3e-78 and 0.0; identity: 95.60%, 91.67% and 98.62%, respectively, as determined by blastp ; Figure 1A, Altschul et al. , 1990). The putative ortholog of Ilp2 is flanked downstream by LOC6737492 (XP_002084328.1), LOC6737493 (XP_002084329.1), LOC6737496 (XP_002084332.2) nested by LOC6737495 (XP_039149023.1), and LOC27207929 (XP_016031291.1), which correspond to Ilp3 , Ilp4, Ilp5, CG43897, and I-2 in D. melanogaster (E-value: 4e-59, 2e-58, 5e-52, 0.0, and 1e-128; identity: 98.33%, 97.35%, 97.22%, 92.64%, and 91.32% respectively, as determined by blastp ). The putative ortholog assignment for Ilp2 in D. simulans is supported by the following evidence: The genes surrounding the Ilp2 ortholog are orthologous to the genes at the same locus in D. melanogaster and local synteny is completely conserved, supported by e-values and percent identities, so we conclude that LOC6737491 is the correct ortholog of Ilp2 in D. simulans (Figure 1A).

Protein Model

Consistent with the blastp search result which shows 97.81% identity between D. melanogaster Ilp2-PA and the D. simulans gene model as well as the low sensitivity parameters used to generate the dot plot (i.e., word size = 3; neighborhood threshold = 11), the dot plot of the two protein sequences contain multiple short gaps along the diagonal (Figure 1C).The red and yellow boxes in the dot plot (Box Y, Box Z; Figure 1C) show lack of sequence similarity between single amino acids near the beginning and middle of coding exon two. Ilp2 in D. simulans has one protein-coding isoform (Ilp2-PA; Figure 1B). Isoform (Ilp2-PA) contains two protein-coding exons. Relative to the ortholog in D. melanogaster , the coding-exon number is conserved. The sequence of Ilp2-PA in D. simulans has 97.81% identity (E-value: 5e-97) with the protein-coding isoform Ilp2-PA in D. melanogaster , as determined by blastp (Figure 1C). Coordinates of this curated gene model are stored by NCBI at GenBank/BankIt (accession BK059551). These data are also archived in the CaltechDATA repository (see “Extended Data” section below).

Extended Data

Description: FASTA, PEP, GFF. Resource Type: Model. DOI: 10.22002/qs6vt-d5d09

Acknowledgments

Acknowledgments

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model, Madeline Gruys for retrofitting this model and Laura K. Reed for overseeing the project.

Funding

This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/; PI-LKR). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health.

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bock, I.R., Wheeler, M.R. (1972). The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1--102. FBrf0024428
  3. Brogiolo W, Stocker H, Ikeya T, Rintelen F, Fernandez R, Hafen E. An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr Biol. 2001 Feb 20;11(4):213–221. doi: 10.1016/s0960-9822(01)00068-9. [DOI] [PubMed] [Google Scholar]
  4. Drosophila 12 Genomes Consortium. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203–218. doi: 10.1038/nature06341. [DOI] [PubMed] [Google Scholar]
  5. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature. 2010 Dec 22;471(7339):473–479. doi: 10.1038/nature09715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Grewal SS. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol. 2008 Oct 18;41(5):1006–1010. doi: 10.1016/j.biocel.2008.10.010. [DOI] [PubMed] [Google Scholar]
  7. Grönke S, Clarke DF, Broughton S, Andrews TD, Partridge L. Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet. 2010 Feb 26;6(2):e1000857–e1000857. doi: 10.1371/journal.pgen.1000857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hietakangas V, Cohen SM. Regulation of tissue growth through nutrient sensing. Annu Rev Genet. 2009;43:389–410. doi: 10.1146/annurev-genet-102108-134815. [DOI] [PubMed] [Google Scholar]
  9. Ikeya T, Galic M, Belawat P, Nairz K, Hafen E. Nutrient-dependent expression of insulin-like peptides from neuroendocrine cells in the CNS contributes to growth regulation in Drosophila. Curr Biol. 2002 Aug 6;12(15):1293–1300. doi: 10.1016/s0960-9822(02)01043-6. [DOI] [PubMed] [Google Scholar]
  10. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun 1;12(6):996–1006. doi: 10.1101/gr.229102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lachaise, D., Tsacas, L. (1983). Breeding-sites of tropical African Drosophilids. Ashburner, Carson, Thompson, 1981-1986 d: 221--332. FBrf0038884
  12. Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J, FlyBase Consortium. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res. 2021 Jan 8;49(D1):D899–D907. doi: 10.1093/nar/gkaa1026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lemeunier, F., David, J., Tsacas, L., Ashburner, M. (1986). The melanogaster species group. Ashburner, Carson, Thompson, 1981-1986 e: 147--256. FBrf0043749
  14. Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Powell CC, Nassar LR, Maulding ND, Lee CM, Lee BT, Hinrichs AS, Fyfe AC, Fernandes JD, Diekhans M, Clawson H, Casper J, Benet-Pagès A, Barber GP, Haussler D, Kuhn RM, Haeussler M, Kent WJ. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res. 2021 Jan 8;49(D1):D1046–D1057. doi: 10.1093/nar/gkaa1070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Park S, Alfa RW, Topper SM, Kim GE, Kockel L, Kim SK. A genetic strategy to measure circulating Drosophila insulin reveals genes regulating insulin production and secretion. PLoS Genet. 2014 Aug 7;10(8):e1004555–e1004555. doi: 10.1371/journal.pgen.1004555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Powell, Jeffrey R. "Progress and prospects in evolutionary biology: the Drosophila model." (1997).I
  17. Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2013 Nov 13;30(7):1003–1005. doi: 10.1093/bioinformatics/btt637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rele CP, Sandlin KM, Leung W, Reed LK. (2020). Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol. bioRxiv 2020.12.10.420521 doi: 10.1101/2020.12.12.420521
  19. Ren S, Huang Z, Jiang Y, Wang T. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J Cell Biol. 2017 Nov 29;217(2):517–526. doi: 10.1083/jcb.201706027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sturtevant, A.H., 1919. A new species closely resembling to Drosophila melanogaster. Psyche 26: 488–500. FBrf0000977

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