title: A sperm-specific proteome-scale metabolic network model identifies non-glycolytic genes for energy deficiency in asthenozoospermia.
abstract: About 15% of couples experience difficulty in conceiving a child, of which half of the cases are thought to be male-related. Asthenozoospermia, or low sperm motility, is one of the frequent types of male infertility. Although energy metabolism is suggested to be central to the etiology of asthenozoospermia, very few attempts have been made to identify its underlying metabolic pathways. Here, we reconstructed SpermNet, the first proteome-scale model of the sperm cell by using whole-proteome data and the mCADRE algorithm. The reconstructed model was then analyzed using the COBRA toolbox. Genes were knocked-out in the model to investigate their effect on ATP production. A total of 78 genes elevated ATP production rate considerably of which most encode components of oxidative phosphorylation, fatty acid oxidation, the Krebs cycle, and members of the solute carrier 25 family. Among them, we identified 11 novel genes which have previously not been associated with sperm cell energy metabolism and may thus be implicated in asthenozoospermia. We further examined the reconstructed model by in silico knock out of currently known asthenozoospermia implicated-genes that were not predicted by our model. The pathways affected by knocking out these genes were also related to energy metabolism, confirming previous findings. Therefore, our model not only predicts the known pathways, it also identifies several non-glycolytic genes for deficient energy metabolism in asthenozoospermia. Finally, this model supports the notion that metabolic pathways besides glycolysis such as oxidative phosphorylation and fatty acid oxidation are essential for sperm energy metabolism and if validated, may form a basis for fertility recovery.
  
  
  BACKGROUND
  mCADRE: metabolic context-specificity assessed by deterministic reaction evaluation; ATP: adenosine triphosphate; RNA: ribonucleic acid; FBA: flux balance analysis; FVA: flux variability analysis; DAVID: database for annotation, visualization and integrated discovery; OXPHOS: oxidative phosphorylation; ETC: electron transfer chain; SLC: solute carrier; DLD: dihydrolypoamide dehydrogenase; DLST: dihydrolypoamide S-succinyl transferase; OGDH: oxoglutarate dehydrogenase; CS: citrate synthase; FH: fumarate hydratase; IDH: isocitrate dehydrogenase; SUCLG1: succinate-CoA ligase; SD: succinate dehydrogenase; HADHA: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase, subunit A; HADHB: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase, subunit B; PPA2: pyrophosphatase (inorganic) 2; PPi: inorganic phosphate; GALT: galactose-1-phosphate uridylyltransferase.
authors.affiliation: a Department of Biotechnology, College of Science , University of Tehran , Tehran , Iran.
authors.forename: Arvand
authors.initials: A
authors.lastname: Asghari
authors.affiliation: a Department of Biotechnology, College of Science , University of Tehran , Tehran , Iran.
authors.forename: Sayed-Amir
authors.initials: SA
authors.lastname: Marashi
authors.affiliation: b Faculty of New Sciences and Technology , University of Tehran , Tehran , Iran.
authors.forename: Naser
authors.initials: N
authors.lastname: Ansari-Pour
mesh_terms: D000465:Algorithms; D053627:Asthenozoospermia / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D003198:Computer Simulation; D030562:Databases, Protein; D004734:Energy Metabolism / Q000235:genetics; D005298:Fertility / Q000235:genetics; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005838:Genotype; D006801:Humans; D008297:Male; D008954:Models, Biological; D010641:Phenotype; D060066:Protein Interaction Maps; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D013094:Spermatozoa / Q000378:metabolism* / Q000473:pathology
chemical_list: D020543:Proteome
keywords: ATP production; Asthenozoospermia; energy metabolism; male infertility; model reconstruction; sperm motility