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. 2022 Jul 2;2022:10.17912/micropub.biology.000544. doi: 10.17912/micropub.biology.000544

Drosophila eugracilis – Akt

Ashley Morgan 1, Cole A Kiser 1, Isabel Bronson 2, Hanjun Lin 2, Nicholas Guillette 3, Robert McMahon 3, Jennifer A Kennell 2, Lindsey J Long 3, Laura K Reed 1, Chinmay P Rele 1,§
Reviewed by: GEP Review Panel
PMCID: PMC9287739  PMID: 35856017

Abstract

Gene Model for Akt in the D. eugracilis (DeugGB2) assembly (GCA_000236325.2).

Figure 1.

Figure 1.

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(A) Synteny of genomic neighborhood of Akt in both D. melanogaster as well as D. eugracilis . Gene arrows pointing in the same direction as Akt in both D. eugracilis and D. melanogaster are on the same strand as Akt ; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrow in D. melanogaster that points to the right indicates Akt is on the + strand and the thin underlying arrow pointing to the left in D. eugracilis indicates Akt is on the – strand. White arrows in D. eugracilis indicate orthology to the corresponding gene in D. melanogaster . CG32855 and sxe2 are nested within an intron of Mhc1 in both species. The gene names given in the D. eugracilis gene arrows indicate the orthologous gene in D. melanogaster , while the locus identifiers are specific to D. eugracilis ; (B) Gene Model in UCSC Track Hub (Raney et al., 2014): The gene model in D. eugracilis (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster ), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. eugracilis ), RNA-Seq from adult females (red), adult males (blue), and mixed embryos (purple) (alignment of Illumina RNAseq reads from D. eugracilis ), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. eugracilis RNA-Seq (Chen et al., 2014; PRJNA63469). Splice junctions shown have a minimum read-depth of 10 with 10-49, 50-99, 100-499, 500-999, >1000 supporting reads in blue, green, pink, brown, and red respectively. The custom gene model (User Supplied Track) is indicated in black with exons depicted with boxes and introns with narrow lines (arrows indicate direction of transcription). (C) Dot Plot of amino acid identity for Akt-PC in D. melanogaster ( x -axis) vs. Akt-PC in D. eugracilis ( y -axis). Amino acid number is indicated along the left and bottom; exon number is indicated along the top and right. Each colored rectangle represents an exon. Region 1 indicates a lack of sequence similarity between the two sequences; (D) ROAST Alignments Conservation track within the UCSC Genome Browser. The ROAST Alignments for 28 Drosophila Species track within the UCSC Genome Browser shows the genomic region surrounding the beginning of the Akt-PC isoform in all 28 species shown, demonstrating that the non-canonical start codon for Akt-PC is conserved across the genus.

Description

Introduction

The insulin signaling pathway is a highly conserved pathway in animals, and is central to nutrient uptake (Hietakangas and Cohen 2009, Grewal 2009). Akt kinase ( Akt also known as Akt1, Protein Kinase B, PKB; FBgn0010379) regulates stress response, aging, and cell growth and survival in Drosophila (Stavely et al ., 1998; Verdu et al. , 1999). It is involved in signal transduction pathways in physiological and neurological pathways in Drosophila (Guo and Zhong 2006). It encodes a core serine-threonine kinase (Bellacosa et al. 1991) component of the Insulin-like growth factor pathway that functions downstream of, and following its activation by the Pi3K92E product in Drosophila (Andjelkovic et al., 1995). It is activated by phosphatidylinositol binding and phosphorylation (Potter et al ., 2002). The gene model reported ( Deug_Akt ) was determined in the Apr. 2013 (BCM-HGSC/Deug_2.0; GCA_000236325.2) of D. eugracilis and compared to the ortholog dmel_Akt (GCA_000001215.4, FB2021_02; Larkin et al., 2021). D. eugracilis is part of the melanogaste r species group within the subgenus Sophophora of Drosophila (Pélandakis et al., 1993). It was first described as Tanygastrella gracilis by Duda (1924) and revised to Drosophila eugracilis by Bock and Wheeler (1972). D. eugracilis is found in humid tropical and subtropical forests across southeast Asia (https://www.taxodros.uzh.ch). The methods and dataset versions used to establish the gene model are described in Rele et al . (2020). 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 http://gander.wustl.edu .The predicted gene model in D. eugracilis for Akt was found in NCBI RefSeq Accession XM_017228041.1 and Locus ID LOC108116251.

Synteny

Akt is located on chromosome 3R (Muller element D) in D. melanogaster and is surrounded by sxe2, CG32855, and Mhcl (upstream) and Sb and CG5903 (downstream). After performing a tblastn , the putative Akt ortholog (LOC10811625/XM_017228041.1/XP_017083530.1, e-value of 0.0 and percent identity of 90.39%) in D. eugracilis was found to be on scaffold KB465333 (mapped to Muller element D) and is surrounded by orthologs to sxe2 (LOC108116355/XM_017228178.2/XP_017083667.2, e-value of 0.0 and percent identity of 87.08%), Mhcl (LOC108116352/XM_017228167.2/XP_017083656.2, e-value of 0.0 and percent identity of 97.13%), Sb (LOC108116404/XM_017228281.2/XP_017083770.2, e-value of 0.0 and percent identity of 87.02%), and CG5903 ( Mic26-27 /LOC108116407/XM_017228287.1/XP_017083776.1, e-value of 7e-151 and percent identity of 88.26%) as determined by blastp (Figure 1A, Altschul et al. , 1990). The annotated model is likely to be the true ortholog of Akt due to the high level of synteny that exists between D. melanogaster and D. eugracilis , and the reciprocal best blast hits between the two genes.

Protein Model

There are five RNA isoforms of Akt : Akt-RA, Akt-RB, Akt-RC, Akt-RD, and Akt-RE . The RA, RB, RD, and RE isoforms have identical protein coding sequences, represented by the Akt-PE protein isoform here. The Akt-PC coding sequence is unique. Both the Akt-PC and Akt-PE isoforms in D. melanogaster are encoded by six coding exons. The Akt-PC and Akt-PE isoforms in D. eugracilis are encoded by six coding exons ( Figure 1B). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accessions BK059589, BK059590, BK059591, BK059592, and BK059593, one for each protein-coding isoform of Akt . These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the gene model

Non-canonical Start Codon: The Akt-RC isoform has a non-canonical ACG start codon. This is well conserved across the 28 Drosophila species as shown in Figure 1D. This non-canonical start codon is used for the translation of the Akt-PC isoform in D. melanogaster , (Figure 1D). There is a high level of conservation of the non-canonical ACG start codon (encoding threonine) across all 28 Drosophila species, as well as high conservation of the region surrounding the non-canonical start codon. This provides evidence for the existence of a non-canonical start codon in the Akt-PC isoform in D. eugracilis .

Methods

Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2020).

Reagents

NA

Extended Data

Description: GTF. Resource Type: Model. DOI: 10.22002/D1.20201

Description: FAA. Resource Type: Model. DOI: 10.22002/D1.20202

Description: FNA. Resource Type: Model. DOI: 10.22002/D1.20203

Acknowledgments

Acknowledgments

We would like to thank Wilson Leung, who created and maintain the GEP technological infrastructure. We would also like to thank Rachael A. Cowan for helping us submit the microPublication and data to NCBI, and Alyssa C. Koehler and Abigail R. Myers for their input on drafting the microPublication.

Funding

This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institute of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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