bims-cytox1 2020-08-09 papers

Issue of 2020–08–09
five papers selected by
Gavin McStay, Staffordshire University

Plant Physiol. 2020 Aug 05. pii: pp.01248.2019. [Epub ahead of print]

The OXA2a Insertase of Arabidopsis Is Required for Cytochrome c Maturation.

Renuka Kolli, Carina Engstler, Sebnem Akbas, Jeffrey P Mower, Jürgen Soll, Christopher Carrie.

In yeast and human mitochondria, Oxa1 (Oxidase assembly protein 1) is the general insertase for protein insertion from the matrix side into the inner membrane while Cox18 (Cytochrome c oxidase assembly protein 18) /Oxa2 is specifically involved in the topogenesis of the complex IV subunit, Cox2. Arabidopsis thaliana mitochondria contain four OXA homologs: OXA1a, OXA1b, OXA2a and OXA2b. OXA2a and OXA2b are unique members of the Oxa1 superfamily, in that they possess a tetratricopeptide repeat (TPR) domain at their C-termini. Here, we determined the role of OXA2a by studying viable mutant plants generated by partial complementation of homozygous lethal OXA2a transfer-DNA insertional mutants using the developmentally regulated ABSCISIC ACID INSENSITIVE3 (ABI3) promoter. The ABI3p:OXA2a plants displayed growth retardation due to a reduction in the steady state abundances of both c-type cytochromes, cytochrome c1 and cytochrome c. The observed reduction in the steady state abundance of complex III could be attributed to cytochrome c1 being one of its subunits. Expression of a soluble heme lyase from an organism with cytochrome c maturation system III could functionally complement the lack of OXA2a. This implies that OXA2a is required for the system I cytochrome c maturation of Arabidopsis. Due to the interaction of OXA2a with CCMFC (Cytochrome c maturation protein CcmF C-terminal-like protein) in a yeast split-ubiquitin based interaction assay, we propose that OXA2a aids in the membrane insertion of CCMFC, which is presumed to form the heme lyase component of the cytochrome c maturation pathway. In contrast to the crucial role played by the TPR domain of OXA2b, the TPR domain of OXA2a is not essential for its functionality.

DOI: https://doi.org/10.1104/pp.19.01248

Metab Brain Dis. 2020 Aug 01.

Mitochondrial genome variation in male LHON patients with the m.11778G > A mutation.

Agnieszka Piotrowska-Nowak, Maciej R Krawczyński, Ewa Kosior-Jarecka, Anna M Ambroziak, Magdalena Korwin, Monika Ołdak, Katarzyna Tońska, Ewa Bartnik.

Leber hereditary optic neuropathy (LHON) is a mitochondrial disorder with symptoms limited to a single tissue, optic nerve, resulting in vision loss. In the majority of cases it is caused by one of three point mutations in mitochondrial DNA (mtDNA) but their presence is not sufficient for disease development, since ~50% of men and ~10% women who carry them are affected. Thus additional modifying factors must exist. In this study, we use next generation sequencing to investigate the role of whole mtDNA variation in male Polish patients with LHON and m.11778G > A, the most frequent LHON mutation. We present a possible association between mtDNA haplogroup K and variants in its background, a combination of m.3480A > G, m.9055G > A, m.11299 T > C and m.14167C > T, and LHON mutation. These variants may have a negative effect on m.11778G > A increasing its penetrance and the risk of LHON in the Polish population. Surprisingly, we did not observe associations previously reported for m.11778G > A and LHON in European populations, particularly for haplogroup J as a risk factor, implying that mtDNA variation is much more complex. Our results indicate possible contribution of novel combination of mtDNA genetic factors to the LHON phenotype.

Keywords: Leber hereditary optic neuropathy (LHON); M.11778G > A mutation; Mitochondrial DNA (mtDNA); Next generation sequencing (NGS); Risk factors

DOI: https://doi.org/10.1007/s11011-020-00605-3

Front Cell Dev Biol. 2020 ;8 617

Using Expansion Microscopy to Visualize and Characterize the Morphology of Mitochondrial Cristae.

Tobias C Kunz, Ralph Götz, Shiqiang Gao, Markus Sauer, Vera Kozjak-Pavlovic.

Mitochondria are double membrane bound organelles indispensable for biological processes such as apoptosis, cell signaling, and the production of many important metabolites, which includes ATP that is generated during the process known as oxidative phosphorylation (OXPHOS). The inner membrane contains folds called cristae, which increase the membrane surface and thus the amount of membrane-bound proteins necessary for the OXPHOS. These folds have been of great interest not only because of their importance for energy conversion, but also because changes in morphology have been linked to a broad range of diseases from cancer, diabetes, neurodegenerative diseases, to aging and infection. With a distance between opposing cristae membranes often below 100 nm, conventional fluorescence imaging cannot provide a resolution sufficient for resolving these structures. For this reason, various highly specialized super-resolution methods including dSTORM, PALM, STED, and SIM have been applied for cristae visualization. Expansion Microscopy (ExM) offers the possibility to perform super-resolution microscopy on conventional confocal microscopes by embedding the sample into a swellable hydrogel that is isotropically expanded by a factor of 4-4.5, improving the resolution to 60-70 nm on conventional confocal microscopes, which can be further increased to ∼ 30 nm laterally using SIM. Here, we demonstrate that the expression of the mitochondrial creatine kinase MtCK linked to marker protein GFP (MtCK-GFP), which localizes to the space between the outer and the inner mitochondrial membrane, can be used as a cristae marker. Applying ExM on mitochondria labeled with this construct enables visualization of morphological changes of cristae and localization studies of mitochondrial proteins relative to cristae without the need for specialized setups. For the first time we present the combination of specific mitochondrial intermembrane space labeling and ExM as a tool for studying internal structure of mitochondria.

Keywords: Expansion microscopy; cristae; mitochondria; structured illumination microscope; ultrastructure

DOI: https://doi.org/10.3389/fcell.2020.00617

Elife. 2020 Aug 07. pii: e57814. [Epub ahead of print]9

Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis.

Tatsuhisa Tsuboi, Matheus P Viana, Fan Xu, Jingwen Yu, Raghav Chanchani, Ximena G Arceo, Evelina Tutucci, Joonhyuk Choi, Yang S Chen, Robert H Singer, Susanne M Rafelski, Brian M Zid.

Mitochondria are dynamic organelles that must precisely control their protein composition according to cellular energy demand. Although nuclear-encoded mRNAs can be localized to the mitochondrial surface, the importance of this localization is unclear. As yeast switch to respiratory metabolism, there is an increase in the fraction of the cytoplasm that is mitochondrial. Our data point to this change in mitochondrial volume fraction increasing the localization of certain nuclear-encoded mRNAs to the surface of the mitochondria. We show that mitochondrial mRNA localization is necessary and sufficient to increase protein production to levels required during respiratory growth. Furthermore, we find that ribosome stalling impacts mRNA sensitivity to mitochondrial volume fraction and counterintuitively leads to enhanced protein synthesis by increasing mRNA localization to mitochondria. This points to a mechanism by which cells are able to use translation elongation and the geometric constraints of the cell to fine-tune organelle-specific gene expression through mRNA localization.

Keywords: S. cerevisiae; cell biology; chromosomes; gene expression; mRNA localization; mitochondria; protein synthesis

DOI: https://doi.org/10.7554/eLife.57814

Mitochondrial DNA A DNA Mapp Seq Anal. 2020 Aug 05. 1-14

Codon usage pattern and its influencing factors for mitochondrial CO genes among different classes of Arthropoda.

Riazul Islam Barbhuiya, Arif Uddin, Supriyo Chakraborty.

Analysis of codon usage bias (CUB) is very much important in perceiving the knowledge of molecular biology, the discovery of a new gene, designing of transgenes and evolution of gene. In this study, we analyzed compositional features and codon usage of MT-CO (COI, COII and COIII) genes among the classes of Arthropoda to explore the pattern of CUB as no research work was reported yet. Nucleotide composition analysis in CO genes suggested that the genes were AT-rich in all the four classes of Arthropoda. CUB was low in all the classes of Arthropoda for MT-CO genes as revealed from a high effective number of codons (ENC). We also found that the evolutionary forces namely mutation pressure and natural selection were the key influencing factors in CUB among MT-CO genes as revealed by correlation analysis between overall nucleotide composition and nucleotide composition at the 3rd codon position. Correspondence analysis suggested that the pattern of CUB was different among the classes of Arthropoda. Further, it was revealed from the neutrality plot that natural selection had a dominant role while mutation pressure exhibited a minor role in structuring the pattern of codon usage in all the classes of Arthropoda across COI, COII and COIII genes.

Keywords: Codon usage bias; cytochrome oxidase gene; electron transport system; mutation pressure; natural selection

DOI: https://doi.org/10.1080/24701394.2020.1800661