bims-tricox 2023-04-09 papers

Issue of 2023‒04‒09
five papers selected by
Yash Verma
University of Delhi South Campus

FEBS Lett. 2023 Apr 05.

Protein translocation in mitochondria: Sorting out the Toms, Tims, Pams, Sams and Mia.

Mitochondria contain 902 (yeast) to 1.136 (mouse, humans) verified proteins. Except for a very small number of mitochondrially encoded core components of the respiratory chain, mitochondrial proteins are encoded by nuclear genes and synthesized in the cytosol. Different import pathways direct proteins to their respective mitochondrial subcompartment (outer membrane, intermembrane space (IMS), inner membrane and matrix). Specific targeting signals in their sequence direct proteins to their target destination and allow the proteins to embark on their respective import pathway. The main import pathways are shown here on the poster and are introduced in the following, using the mitochondrial import system of the baker's yeast Saccharomyces cerevisiae as example. However, the mitochondrial import system of mammalian cells is highly similar and deviates only in minor aspects. Even the mitochondrial import machineries of less closely related eukaryotes, such as plants and trypanosomes, are very similar and adhere to the same general principles.

Keywords: Mitochondria; Protein Import; Protein translocation; Translocase of the inner membrane; Translocase of the outer membrane

DOI: https://doi.org/10.1002/1873-3468.14614

PNAS Nexus. 2023 Mar;2(3): pgad074

Optimization of ribosome utilization in Saccharomyces cerevisiae.

Mahima, Ajeet K Sharma.

Resource optimization in protein synthesis is often looked at from the perspective of translation efficiency-the rate at which proteins are synthesized from a single transcript. The higher the rate of protein synthesis, the more efficiently a transcript is translated. However, the production of a ribosome consumes significantly more cellular resources than an mRNA molecule. Therefore, there should be a stronger selection pressure for optimizing ribosome usage than translation efficiency. This paper reports strong evidence of such optimization which becomes more prominent in highly expressed transcripts that consume a significant amount of cellular resources. The ribosome usage is optimized by the biases in codon usage and translation initiation rates. This optimization significantly reduces the ribosome requirement in Saccharomyces cerevisiae. We also find that a low ribosome density on mRNA transcripts helps optimize ribosome utilization. Therefore, protein synthesis occurs in a low ribosome density regime where translation-initiation is the rate-limiting step. Our results suggest that optimizing ribosome usage is one of the major forces shaping evolutionary selection pressure, and thus provide a new perspective to resource optimization in protein synthesis.

DOI: https://doi.org/10.1093/pnasnexus/pgad074

Physiol Rep. 2023 Apr;11(7): e15632

TOM complex-independent transport pathway of myoglobin into mitochondria in C2C12 myotubes.

Rikuhide Koma, Tsubasa Shibaguchi, Yuhei Araiso, Tatsuya Yamada, Yudai Nonaka, Thomas Jue, Kazumi Masuda.

Recently, we found that myoglobin (Mb) localizes in both the cytosol and mitochondrial intermembrane space in rodent skeletal muscle. Most proteins of the intermembrane space pass through the outer mitochondrial membrane via the translocase of the outer membrane (TOM) complex. However, whether the TOM complex imports Mb remains unknown. The purpose of this study was to investigate the involvement of the TOM complex in Mb import into the mitochondria. A proteinase K protection assay of mitochondria from C2C12 myotubes confirmed that Mb integrated into the mitochondria. An immunoprecipitation assay verified the interaction of Mb and TOM complex receptors (Tom20, Tom70) in isolated mitochondria. The assay showed a clear interaction of Mb with Tom20 and Tom70. A knockdown experiment using siRNA for TOM complex receptors (Tom20, Tom70) and TOM complex channel (Tom40) did not alter the amount of Mb expression in the mitochondrial fraction. These results suggested that Mb does not necessarily require the TOM complex for mitochondrial import of Mb. Although the physiological role of Mb interactions with TOM complex receptors remains unclear, further studies are needed to clarify how Mb enters the mitochondria independently of the TOM complex.

Keywords: Tom20; Tom40; Tom70; skeletal muscle

DOI: https://doi.org/10.14814/phy2.15632

Microb Cell. 2023 Apr 03. 10(4): 78-87

A modular cloning (MoClo) toolkit for reliable intracellular protein targeting in the yeast Saccharomyces cerevisiae.

Pavel Simakin, Christian Koch, Johannes M Herrmann.

Modular Cloning (MoClo) allows the combinatorial assembly of plasmids from standardized genetic parts without the need of error-prone PCR reactions. It is a very powerful strategy which enables highly flexible expression patterns without the need of repetitive cloning procedures. In this study, we describe an advanced MoClo toolkit that is designed for the baker's yeast Saccharomyces cerevisiae and optimized for the targeting of proteins of interest to specific cellular compartments. Comparing different targeting sequences, we developed signals to direct proteins with high specificity to the different mitochondrial subcompartments, such as the matrix and the intermembrane space (IMS). Furthermore, we optimized the subcellular targeting by controlling expression levels using a collection of different promoter cassettes; the MoClo strategy allows it to generate arrays of expression plasmids in parallel to optimize gene expression levels and reliable targeting for each given protein and cellular compartment. Thus, the MoClo strategy enables the generation of protein-expressing yeast plasmids that accurately target proteins of interest to various cellular compartments.

Keywords: expression plasmids; mitochondrial import; modular cloning; promoter strength; protein targeting; split GFP

DOI: https://doi.org/10.15698/mic2023.04.794

Exp Gerontol. 2023 Apr 05. pii: S0531-5565(23)00086-4. [Epub ahead of print]176 112165

Mediterranean diet and mitochondria: New findings.

Francesco Pollicino, Nicola Veronese, Ligia J Dominguez, Mario Barbagallo.

Mitochondria are subcellular organelles known for their central role in several energetic processes. Accumulating evidence supports a key role for mitochondria in the physiological response to both acute and chronic stress exposure, and, ultimately, the biological embedding of adversity in health and psychological functioning that increases the interest of these organelles in several medical conditions typical of older people. At the same time, Mediterranean diet (MedDiet) seems to affect the function of mitochondria further justifying the role of this diet in lowering the risk of negative health outcomes. In this review, we have elucidated the role of mitochondria in human diseases including the fundamental role in stress, aging, and neuropsychiatric and metabolic disorders. Overall, MedDiet can limit the production of free radicals, being rich in polyphenols. Moreover, MedDiet reduced mitochondrial reactive oxygen species (mtROS) production and ameliorated mitochondrial damage and apoptosis. Similarly, whole grains can maintain the mitochondrial respiration and membrane potential, finally improving mitochondrial function. Other components of MedDiet can have anti-inflammatory effects, again modulating mitochondrial function. For example, delphinidin (a flavonoid present in red wine and berries) restored the elevated level of mitochondrial respiration, mtDNA content, and complex IV activity; similarly, resveratrol and lycopene, present in grapefruits and tomatoes, exerted an anti-inflammatory effect modulating mitochondrial enzymes. Altogether, these findings support the notion that several positive effects of MedDiet can be mediated by a modulation in mitochondrial function indicating the necessity of further studies in human beings for finally confirming these findings.

Keywords: Dementia; Inflammation; Mediterranean diet; Metabolic syndrome; Mitochondria; Stress

DOI: https://doi.org/10.1016/j.exger.2023.112165