The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context

Marchianò, Fabio; Haering, Margaux; Habermann, Bianca

doi:10.1093/nar/gkac306

Cited by 20 publications

(9 citation statements)

References 43 publications

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“…Data 6). The individual profiles were normalised using the sum of iBAQ values of the identified proteins annotated as mitochondrial in MitoCarta 3.0 (21) and/or mitoXplorer 2.0 (22) and/or as "verified/associated" in the Integrated Mitochondrial Protein Index (IMPI) (23), excluding the subunits of OXPHOS complexes I, III, IV, V and mitoribosomes. Calibration curves of apparent molecular masses was performed as described previously (24) using human membrane and water-soluble protein complexes of known masses (e.g., OXPHOS complexes, VDACs, HSP60, OGDH; for details see Suppl.…”

Section: Complexome Profilingmentioning

confidence: 99%

Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling

Potter¹,

Cabrera‐Orefice

Spelbrink³

2023

Preprint

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Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimised this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multi-protein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically-induced mtDNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.

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Section: Complexome Profilingmentioning

confidence: 99%

Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling

Potter¹,

Cabrera‐Orefice

Spelbrink³

2023

Preprint

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“…Both packages were additionally used to generate normalized counts values. We employed previously annotated sets of genes, including sarcomere proteins [ 42 ], genes with an RNAi phenotype in muscle [ 153 ], core fibrillar genes regulated by Spalt major and differentially expressed between IFM and tubular muscle [ 14 ], mitochondrial proteins [ 104 , 161 ], and all genes with the Flybase GO term “muscle contraction,” “actin cytoskeleton,” or “actin cytoskeleton organization.” Genes with a hypercontraction phenotype in Drosophila muscle were curated by hand from the literature. Full lists of all gene categories are available in S2 Table .…”

Section: Methodsmentioning

confidence: 99%

Bruno 1/CELF regulates splicing and cytoskeleton dynamics to ensure correct sarcomere assembly in Drosophila flight muscles

Nikonova,

DeCata,

Canela

et al. 2024

PLoS Biol

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Muscles undergo developmental transitions in gene expression and alternative splicing that are necessary to refine sarcomere structure and contractility. CUG-BP and ETR-3-like (CELF) family RNA-binding proteins are important regulators of RNA processing during myogenesis that are misregulated in diseases such as Myotonic Dystrophy Type I (DM1). Here, we report a conserved function for Bruno 1 (Bru1, Arrest), a CELF1/2 family homolog in Drosophila, during early muscle myogenesis. Loss of Bru1 in flight muscles results in disorganization of the actin cytoskeleton leading to aberrant myofiber compaction and defects in pre-myofibril formation. Temporally restricted rescue and RNAi knockdown demonstrate that early cytoskeletal defects interfere with subsequent steps in sarcomere growth and maturation. Early defects are distinct from a later requirement for bru1 to regulate sarcomere assembly dynamics during myofiber maturation. We identify an imbalance in growth in sarcomere length and width during later stages of development as the mechanism driving abnormal radial growth, myofibril fusion, and the formation of hollow myofibrils in bru1 mutant muscle. Molecularly, we characterize a genome-wide transition from immature to mature sarcomere gene isoform expression in flight muscle development that is blocked in bru1 mutants. We further demonstrate that temporally restricted Bru1 rescue can partially alleviate hypercontraction in late pupal and adult stages, but it cannot restore myofiber function or correct structural deficits. Our results reveal the conserved nature of CELF function in regulating cytoskeletal dynamics in muscle development and demonstrate that defective RNA processing due to misexpression of CELF proteins causes wide-reaching structural defects and progressive malfunction of affected muscles that cannot be rescued by late-stage gene replacement.

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“…Genes that were significantly differentially expressed were defined as those with a false discovery rate (FDR) q-value of <0.05. Mitochondrial genes in the DEG dataset were extracted along with their annotations in mitoXplorer 2.0 (35, 36). We determined enrichment with PANGEA (37) using all DEGs as the test set, all expressed genes (Supplemental Table S3) as the background, and gene set categories of ‘KEGG Pathway D. mel’, ‘Preferred tissue (modEncode RNA_seq)’, and all three Drosophila GOslim gene sets (Biological Process, Cellular Component, Molecular Function).…”

Section: Methodsmentioning

confidence: 99%

The intracellular symbiontWolbachiaaltersDrosophiladevelopment and metabolism to buffer against nutritional stress

Lindsey

Parish

Newton

et al. 2023

Preprint

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Approximately a quarter of eukaryotes are infected with the bacterium Wolbachia. Its broad success as a vertically transmitted infection has been historically difficult to explain given the myriad of parasitic impacts characterized across Wolbachia's host range. Using the Drosophila model and their natively associated Wolbachia, we show that Wolbachia infection supports fly development and buffers against nutritional stress. Wolbachia infection across several fly genotypes and a range of nutrient conditions resulted in reduced pupal mortality, increased adult emergence, and larger size. We determined that the exogenous supplementation of pyrimidines rescued these phenotypes in the Wolbachia-free, flies suggesting that Wolbachia plays a role in providing this metabolite that is normally limiting for insect growth. Additionally, Wolbachia was sensitive to host pyrimidine metabolism: Wolbachia titers increased upon transgenic knockdown of the Drosophila de novo pyrimidine synthesis pathway but not knockdown of the de novo purine synthesis pathway. We propose that Wolbachia acts as a nutritional symbiont to supplement insect development and increase host fitness: a selective advantage that could contribute to its high frequency in nature.

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The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context

Cited by 20 publications

References 43 publications

Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling

Let’s make it clear: Systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling

Bruno 1/CELF regulates splicing and cytoskeleton dynamics to ensure correct sarcomere assembly in Drosophila flight muscles

The intracellular symbiontWolbachiaaltersDrosophiladevelopment and metabolism to buffer against nutritional stress

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