Machinery for mitochondrial cholesterol transport for steroidogenesis and functional prediction.

<p>A. Schematic diagram of the transduceosome, steroidogenic metabolon, and associated signal transduction proteins and their likely roles in mitochondrial cholesterol transport and cholesterol metabolism into the first intermediate product, pregnenolone, during steroidogenesis. Each member and the closest members in their corresponding gene family were selected for further evolutionary analysis. IMM, inner mitochondrial membrane; IMS, intermembrane space; OMM, outer mitochondrial membrane. B. Orthologous origin of human TSPO-mediated steroidogenesis complex proteins in other animals. The proteins include Translocator Protein 18-kDa (TSPO) previously known as peripheral benzodiazepine receptor (PBR or BZRP), steroidogenic acute regulatory protein (STAR) or START domain containing 1 (STAR/STARD1), acyl-CoA binding domain containing 3 or PBR- and PKA-associated protein 7 (ACBD3/PAP7), cytochrome P450, family 11, subfamily A, polypeptide 1 (CYP11A1), acyl-CoA binding domain containing 1 or diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein; ACBD1/DBI), protein kinase, cAMP-dependent, regulatory, type I, alpha (PRKAR1A), ATPase family, AAA domain containing 3A (ATAD3), mitogen-activated protein kinase 3 or extracellular signal-regulated kinase ½ (MAPK3/ERK1/2), acyl-CoA synthetase long-chain family member 4 (ACSL4), acyl-CoA thioesterase 2/3 (ACOT2/3), voltage-dependent anion channel 1 (VDAC1), adenine nucleotide translocator 1 or solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 (ANT1/SLC25A4). BLAST expectation value (<i>e</i>-value), a statistical calculation based on the score that gives the number of hits that this search would return by chance in a genome database, was used in the ranking of the best matches (“hits”) from the database. A higher e-value may suggest a distant evolutionary relationship. The max identity (percent similarity between the query and subject sequences over the length of the coverage area) was used to show the occurrence of the proteins in the organism as ink blots of the heatmap where the diameter of each dot corresponds to the value. That is, the ink blot is smallest exactly halfway between the minimum and maximum values and becomes progressively larger as the values approach the minimum or maximum. Green to red indicates the value (%) from smaller to bigger. The data was normalized in each row. C. The <i>in </i><i>silico</i> prediction of functional divergence in protein evolution by site-specific rate shifts using the maximum likelihood method in DIVERGE [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076701#B29" target="_blank">29</a>]. G1-G3, paralogous gene number 1 to 3; IV, invertebrate; V, vertebrate; H₀ and H₁, hypothesis of the type I evolutionary functional divergence using a coefficient of statistical divergence (θ), which is the change in function that resulted from different rates at these sites between clusters. If the null hypothesis of θ = 0 was not rejected, the evolutionary rate is virtually the same between two clusters of genes, and this result implies that these clusters share the same function(s). The dotted line indicates that gene duplication did not occur.