Respiratory chain alternative enzymes form additional pathways of the mitochondrial oxidative phosphorylation process (OXPHOS), in which oxygen consumption is uncoupled of ATP synthesis. The expression of the alternative oxidase (AOX) and the alternative NADH dehydrogenase from the tunicate Ciona intestinalis (Ascidiacea) in the fly Drosophila melanogaster, mouse and human cells in culture has been showing effective against deleterious effects caused OXPHOS deficiency. Organisms that have alternative enzymes like C. intestinalis, may have accumulated more deleterious nucleotide substitution in the genes that encode the respiratory chain subunits, because the presence of alternative enzymes can allow the organism to survive and reproduce even with these deleterious mutations. The objective is to use bioinformatic tools to explore the genome of C. intestinalis, identifying the genes to build a "virtual respiratory chain" of this organism's mitochondria, and to analyze the molecular evolution rates of each gene of this system, comparing them with the ones of humans and D. melanogaster. We intend to infer how the presence of respiratory chain alternative enzymes may change the composition and the evolutionary pattern of the genes and proteins which constitute it. The hypothesis is that the genes and proteins of the respiratory chain of C. intestinalis evolve faster, accumulating more slightly deleterious mutations, or being discarded from the genome because of the presence of alternative enzymes. Initially, two approaches will be used to recover the mitochondrial genes of C. intestinalis and then build the "virtual respiratory chain" of this organism 1) the genes that encode the respiratory chain proteins of humans and D. melanogaster will be used as template to search for orthologous genes using BLAST in the genome of C. intestinalis and Ciona savignyi, which is a closely related species; and 2) All the sequences of proteins encoded by all Identified mitochondrial genes will be used to search mitochondrial location signs with the help of softwares like MITOPROT and TargetP, to improve the accuracy of the genes selected after the use of BLAST. The direct comparison between the complex of OXPHOS in humans, D. melanogaster and C. intestinalis will reveal how they are constituted, showing if the presence of alternative enzymes can change the number of subunits of each complex. Beside the changes in the composition of subunits, will be possibly to infer if have quantitative changes in the mitochondrial proteins of C. intestinalis, using the comparison between the evolution rates of nucleotides and amino acids using softwares like MEGA7. The fact of the expression. of alternative enzymes kept the cellular respiration even under the condition of disjunction of the complexes I, III, and IV of OXPHOS, is expected that the genes which encode the subunits of those complexes in C. intestinalis have accumulated more deleterious mutations than the orthologous genes in vertebrates and arthropods.
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