Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system.

Radek Szklarczyk,Rutger Vogel,Jan Smeitink,Robin Van Der Lee,Martijn A Huynen,Hubert J M Smeets

doi:10.1186/s12864-015-1883-8

Abstract

BackgroundTranscriptional control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study we performed RNA sequencing of two control and two complex I-deficient patient cell lines cultured in the presence of compounds that perturb mitochondrial metabolism: chloramphenicol, AICAR, or resveratrol. We combined this with a comprehensive analysis of mitochondrial and nuclear gene expression patterns, co-expression calculations and transcription factor binding sites.ResultsOur analyses show that subsets of mitochondrial OXPHOS genes respond opposingly to chloramphenicol and AICAR, whereas the response of nuclear OXPHOS genes is less consistent between cell lines and treatments. Across all samples nuclear OXPHOS genes have a significantly higher co-expression with each other than with other genes, including those encoding mitochondrial proteins. We found no evidence for complex-specific mRNA expression regulation: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of nuclear genes for OXPHOS subunits versus assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of novel candidates (ELK1, KLF7, SP4, EHF, ZNF143, and TEL2).ConclusionsOXPHOS genes share an expression program distinct from other genes encoding mitochondrial proteins, indicative of targeted nuclear regulation of a mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between mitochondrial and nuclear genes, and between nuclear genes encoding subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1883-8) contains supplementary material, which is available to authorized users.

Highlights

Transcriptional control of mitochondrial metabolism is essential for cellular function
Mitochondria are the primary source of cellular Adenosine triphosphate (ATP), which is generated via electron transfer in the oxidative phosphorylation (OXPHOS) system using substrates derived from oxidation of carbohydrates, fatty acids and amino acids
Incubation and RNA sequencing of complex I-deficient patient cells To investigate patterns of transcription in OXPHOS deficiency, we measured gene expression in two healthy fibroblast cell lines and two fibroblast patient cell lines carrying mutations in complex I genes NDUFS2 and ND5 (Fig. 1)

Summary

Introduction

Transcriptional control of mitochondrial metabolism is essential for cellular function. In this study we performed RNA sequencing of two control and two complex I-deficient patient cell lines cultured in the presence of compounds that perturb mitochondrial metabolism: chloramphenicol, AICAR, or resveratrol. We combined this with a comprehensive analysis of mitochondrial and nuclear gene expression patterns, co-expression calculations and transcription factor binding sites. The value of healthy mitochondria becomes evident in cases of OXPHOS deficiency These metabolic disorders primarily affect tissues with a high ATP demand such as the brain, heart, and skeletal muscle, typically resulting in progressive energy deficiencies and childhood death [1]. There is a great need for a better understanding of how the biogenesis and activity of the OXPHOS system is controlled

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