The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates

Porcelli, Damiano; Barsanti, Paolo; Pesole, Graziano; Caggese, Corrado

doi:10.1186/1471-2148-7-215

Cited by 36 publications

(35 citation statements)

References 51 publications

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“…Enzymes and structural components of the mitochondria are synthesized mainly from the nuclear genome. Mitochondrial enzymes frequently contain duplicates with testis-biased expression patterns for one of them, based on microarray analysis of Drosophila males and females [ 4 , 5 ]. Spermatid mitochondria aggregate, fuse and form the Nebenkern in round spermatids [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Drosophila melanogaster testis transcriptome

et al. 2018

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BackgroundThe formation of matured and individual sperm involves a series of molecular and spectacular morphological changes of the developing cysts in Drosophila melanogaster testis. Recent advances in RNA Sequencing (RNA-Seq) technology help us to understand the complexity of eukaryotic transcriptomes by dissecting different tissues and developmental stages of organisms. To gain a better understanding of cellular differentiation of spermatogenesis, we applied RNA-Seq to analyse the testis-specific transcriptome, including coding and non-coding genes.ResultsWe isolated three different parts of the wild-type testis by dissecting and cutting the different regions: 1.) the apical region, which contains stem cells and developing spermatocytes 2.) the middle region, with enrichment of meiotic cysts 3.) the basal region, which contains elongated post-meiotic cysts with spermatids. Total RNA was isolated from each region and analysed by next-generation sequencing. We collected data from the annotated 17412 Drosophila genes and identified 5381 genes with significant transcript accumulation differences between the regions, representing the main stages of spermatogenesis. We demonstrated for the first time the presence and region specific distribution of 2061 lncRNAs in testis, with 203 significant differences. Using the available modENCODE RNA-Seq data, we determined the tissue specificity indices of Drosophila genes. Combining the indices with our results, we identified genes with region-specific enrichment in testis.ConclusionBy multiple analyses of our results and integrating existing knowledge about Drosophila melanogaster spermatogenesis to our dataset, we were able to describe transcript composition of different regions of Drosophila testis, including several stage-specific transcripts. We present searchable visualizations that can facilitate the identification of new components that play role in the organisation and composition of different stages of spermatogenesis, including the less known, but complex regulation of post-meiotic stages.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5085-z) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Analysis of Drosophila melanogaster testis transcriptome

et al. 2018

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“…OXPHOS and CRP genes. B. mori and D. melanogaster OXPHOS and CRP protein sequences were retrieved (Marygold SJ et al, 2007;Porcelli D et al, 2007) and…”

Section: Genome Assemblymentioning

confidence: 99%

“…All 79 ribosomal proteins conserved between mammals and D. melanogaster (Yoshihama M et al, 2002;Marygold SJ et al, 2007) have orthologs in T. ni, further evidence of the completeness of the genome assembly (Supplementary file 1B). Finally, a search for genes in the highly conserved nuclear oxidative phosphorylation (OXPHOS) pathway (Porcelli D et al, 2007) uncovered T. ni orthologs for all known D. melanogaster OXPHOS genes (Supplementary file 1C).…”

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confidence: 99%

The genome ofTrichoplusia ni, an agricultural pest and novel model for small RNA biology

Yang

Zhang

et al. 2017

Preprint

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The cabbage looper, Trichoplusia ni (Lepidoptera: Noctuidae), is a destructive insect pest that feeds on a wide range of plants. The High Five cell line (Hi5), originally derived from T. ni ovaries, is often used for efficient expression of recombinant proteins. Here, we report a draft assembly of the 368.2 Mb T. ni genome, with 90.6% of all bases assigned to one of its 28 chromosomes and predicted 14,037 predicted protein-coding

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“…Furthermore, a first in silico analysis of D. melanogaster ’s nuclear energy gene sequences has suggested that a single regulatory element, resulting in a genetic regulatory circuit, can coordinate the expression of the whole set of energy-producing genes in this insect [ 28 , 29 ]. This motif is known as Nuclear Respiratory Gene (NRG) element [ 28 , 30 ]. It is a palindromic 8-bp sequence (TTAYRTAA) shared by all the nuclear insect oxidative phosphorylation (OXPHOS) genes, as well as by many other nuclear genes involved in mitochondrial biogenesis and function [ 28 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Drosophila melanogaster Mitochondrial Carriers: Similarities and Differences with the Human Carriers

Curcio

Lunetti

Zara

et al. 2020

IJMS

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Mitochondrial carriers are a family of structurally related proteins responsible for the exchange of metabolites, cofactors and nucleotides between the cytoplasm and mitochondrial matrix. The in silico analysis of the Drosophila melanogaster genome has highlighted the presence of 48 genes encoding putative mitochondrial carriers, but only 20 have been functionally characterized. Despite most Drosophila mitochondrial carrier genes having human homologs and sharing with them 50% or higher sequence identity, D. melanogaster genes display peculiar differences from their human counterparts: (1) in the fruit fly, many genes encode more transcript isoforms or are duplicated, resulting in the presence of numerous subfamilies in the genome; (2) the expression of the energy-producing genes in D. melanogaster is coordinated from a motif known as Nuclear Respiratory Gene (NRG), a palindromic 8-bp sequence; (3) fruit-fly duplicated genes encoding mitochondrial carriers show a testis-biased expression pattern, probably in order to keep a duplicate copy in the genome. Here, we review the main features, biological activities and role in the metabolism of the D. melanogaster mitochondrial carriers characterized to date, highlighting similarities and differences with their human counterparts. Such knowledge is very important for obtaining an integrated view of mitochondrial function in D. melanogaster metabolism.

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The nuclear OXPHOS genes in insecta: a common evolutionary origin, a common cis-regulatory motif, a common destiny for gene duplicates

Cited by 36 publications

References 51 publications

Analysis of Drosophila melanogaster testis transcriptome

Analysis of Drosophila melanogaster testis transcriptome

The genome ofTrichoplusia ni, an agricultural pest and novel model for small RNA biology

Drosophila melanogaster Mitochondrial Carriers: Similarities and Differences with the Human Carriers

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