Quantitative Evaluation of the Mitochondrial Proteomes of Drosophila melanogaster Adapted to Extreme Oxygen Conditions

Abstract

Mitochondria are the primary organelles that consume oxygen and provide energy for cellular activities. To investigate the mitochondrial mechanisms underlying adaptation to extreme oxygen conditions, we generated Drosophila strains that could survive in low- or high-oxygen environments (LOF or HOF, respectively), examined their mitochondria at the ultrastructural level via transmission electron microscopy, studied the activity of their respiratory chain complexes, and quantitatively analyzed the protein abundance responses of the mitochondrial proteomes using Isobaric tag for relative and absolute quantitation (iTRAQ). A total of 718 proteins were identified with high confidence, and 55 and 75 mitochondrial proteins displayed significant differences in abundance in LOF and HOF, respectively, compared with the control flies. Importantly, these differentially expressed mitochondrial proteins are primarily involved in respiration, calcium regulation, the oxidative response, and mitochondrial protein translation. A correlation analysis of the changes in the levels of the mRNAs corresponding to differentially regulated mitochondrial proteins revealed two sets of proteins with different modes of regulation (transcriptional vs. post-transcriptional) in both LOF and HOF. We believe that these findings will not only enhance our understanding of the mechanisms underlying adaptation to extreme oxygen conditions in Drosophila but also provide a clue in studying human disease induced by altered oxygen tension in tissues and cells.

Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase

“…We compared our results with the Drosophila mitochondrial proteome obtained in two previous studies (16,17) that identified proteins from whole mitochondria, including matrix, both mitochondrial membranes, and intermembrane space, following traditional mitochondrial isolation (Fig. 4 E and F and Fig.…”

“…S7). Yin et al (16) identified 718 proteins corresponding to 698 genes based on the FlyBase release 5.54 gene annotation; 49% of these were represented in our positive control list, and 9% were in our negative control list. In addition, Lotz et al (17) identified 1,089 proteins, of which 57% were in our positive control list.…”

“…To build a comprehensive database, MitoMax, for Drosophila mitochondrial proteins with subcompartmental annotation, Drosophila genes identified by either isolation-based studies (16,17) or by our APEX labeling approach were combined and integrated with genes from human annotation (1,290 genes) as well as Drosophila genes annotated at MitoMiner (18) and MitoDrome (19) (Fig. S8; genepath.med.…”

Mitochondrial calcium uniporter regulator 1 (MCUR1) regulates the calcium threshold for the mitochondrial permeability transition

“…PPIF is the most studied MPT regulator, and a Drosophila homolog (Cyp-1) has been isolated in multiple proteomic studies of purified Drosophila mitochondria (18,19) (Fig. S2A).…”

Nature's fat-burning machine: brown adipose tissue in a hibernating mammal

“…However, mRNA levels are not always correlated closely with protein abundance and function in living systems (de Sousa Abreu et al, 2009;Foss et al, 2011;Gry et al, 2009;Nie et al, 2007;Pascal et al, 2008;Yin et al, 2013). Therefore, recent research efforts have involved characterizing global patterns of protein expression of BAT across the circannual cycle in hibernators using various proteomics techniques.…”