Mechanism of super-assembly of respiratory complexes III and IV.

Respiratory chain complexes can super-assemble into quaternary structures called supercomplexes that optimize cellular metabolism. The interaction between complexes III (CIII) and IV (CIV) is modulated by supercomplex assembly factor 1 (SCAF1, also known as COX7A2L). The discovery of SCAF1 represented strong genetic evidence that supercomplexes exist in vivo. SCAF1 is present as a long isoform (113 amino acids) or a short isoform (111 amino acids) in different mouse strains. Only the long isoform can induce the super-assembly of CIII and CIV, but it is not clear whether SCAF1 is required for the formation of the respirasome (a supercomplex of CI, CIII2 and CIV). Here we show, by combining deep proteomics and immunodetection analysis, that SCAF1 is always required for the interaction between CIII and CIV and that the respirasome is absent from most tissues of animals containing the short isoform of SCAF1, with the exception of heart and skeletal muscle. We used directed mutagenesis to characterize SCAF1 regions that interact with CIII and CIV and discovered that this interaction requires the correct orientation of a histidine residue at position 73 that is altered in the short isoform of SCAF1, explaining its inability to interact with CIV. Furthermore, we find that the CIV subunit COX7A2 is replaced by SCAF1 in supercomplexes containing CIII and CIV and by COX7A1 in CIV dimers, and that dimers seem to be more stable when they include COX6A2 rather than the COX6A1 isoform.

zfRegeneration: a database for gene expression profiling during regeneration.

MOTIVATION: Zebrafish is a model organism with the ability to regenerate many different organs. Although RNA-Seq has been used extensively to study this process, there are no databases that allow easy access to data. RESULTS: Here we develop the first regeneration database that provides easy access to a large number of RNA-Seq datasets through custom-made plots of expression levels, differential expression analyses, correlations of genes and comparisons of the different datasets. zfRegeneration has a user-friendly web interface designed to enhance regeneration studies and to overcome the barriers between different research groups that study the regeneration of distinct organs. Using several case studies, we demonstrate that zfRegeneration provides a unique platform to analyse and understand gene expression during regeneration. AVAILABILITY AND IMPLEMENTATION: zfRegeneration is freely available at www.zfregeneration.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart.

Cardiac progenitors are specified early in development and progressively differentiate and mature into fully functional cardiomyocytes. This process is controlled by an extensively studied transcriptional program. However, the regulatory events coordinating the progression of such program from development to maturation are largely unknown. Here, we show that the genome organizer CTCF is essential for cardiogenesis and that it mediates genomic interactions to coordinate cardiomyocyte differentiation and maturation in the developing heart. Inactivation of Ctcf in cardiac progenitor cells and their derivatives in vivo during development caused severe cardiac defects and death at embryonic day 12.5. Genome wide expression analysis in Ctcf mutant hearts revealed that genes controlling mitochondrial function and protein production, required for cardiomyocyte maturation, were upregulated. However, mitochondria from mutant cardiomyocytes do not mature properly. In contrast, multiple development regulatory genes near predicted heart enhancers, including genes in the IrxA cluster, were downregulated in Ctcf mutants, suggesting that CTCF promotes cardiomyocyte differentiation by facilitating enhancer-promoter interactions. Accordingly, loss of CTCF disrupts gene expression and chromatin interactions as shown by chromatin conformation capture followed by deep sequencing. Furthermore, CRISPR-mediated deletion of an intergenic CTCF site within the IrxA cluster alters gene expression in the developing heart. Thus, CTCF mediates local regulatory interactions to coordinate transcriptional programs controlling transitions in morphology and function during heart development.

Ablation of the stress protease OMA1 protects against heart failure in mice.

Heart failure (HF) is a major health and economic burden in developed countries. It has been proposed that the pathogenesis of HF may involve the action of mitochondria. We evaluate three different mouse models of HF: tachycardiomyopathy, HF with preserved left ventricular (LV) ejection fraction (LVEF), and LV myocardial ischemia and hypertrophy. Regardless of whether LVEF is preserved, our results indicate that the three models share common features: an increase in mitochondrial reactive oxygen species followed by ultrastructural alterations in the mitochondrial cristae and loss of mitochondrial integrity that lead to cardiomyocyte death. We show that the ablation of the mitochondrial protease OMA1 averts cardiomyocyte death in all three murine HF models, and thus loss of OMA1 plays a direct role in cardiomyocyte protection. This finding identifies OMA1 as a potential target for preventing the progression of myocardial damage in HF associated with a variety of etiologies.

Septin 4, the drosophila ortholog of human CDCrel-1, accumulates in parkin mutant brains and is functionally related to the Nedd4 E3 ubiquitin ligase.

Parkinson's disease (PD) is the second most common neurodegenerative disorder. Although most PD cases are sporadic, several loci have been involved in the disease. parkin (PARK) is causative of autosomal recessive juvenile Parkinsonism (ARJP) and encodes an E3 ubiquitin ligase associated with proteasomal degradation. It was proposed that loss of PARK function may lead to the toxic accumulation of its substrates in the brain, thus causing dopaminergic (DA) neuron death. Indeed, the first identified PARK substrate was CDCrel-1, a protein of the Septin family that accumulates in ARPJ brains. Drosophila has been used as a successful model organism to study PD broadly contributing to the understanding of the disease. Consistently, park mutant flies recapitulate some key features of ARJP patients. In this scenario, we previously reported that overexpression of Septin 4 (Sep4), the Drosophila ortholog of CDCrel-1, is toxic for DA neurons and interacts physically with Park, thus suggesting that Sep4 could be a Park substrate in Drosophila. Confirming this hypothesis, we show that Sep4 accumulates in park mutant brains as its human counterpart. Furthermore, we demonstrate that Nedd4, another E3 ubiquitin ligase that may have a role in PD, is functionally related to Sep4 and could be involved in regulating Sep4 subcellular localization/trafficking.