bims-smemid 2025-04-20 papers

Cell Rep Methods. 2025 Apr 08. pii: S2667-2375(25)00063-3. [Epub ahead of print] 101027

Integrated analysis of transcriptional and metabolic responses to mitochondrial stress.

Liam P Kelley, Song-Hua Hu, Sarah A Boswell, Peter K Sorger, Alison E Ringel, Marcia C Haigis.

Mitochondrial stress arises from a variety of sources, including mutations to mitochondrial DNA, the generation of reactive oxygen species, and an insufficient supply of oxygen or fuel. Mitochondrial stress induces a range of dedicated responses that repair damage and restore mitochondrial health. However, a systematic characterization of transcriptional and metabolic signatures induced by distinct types of mitochondrial stress is lacking. Here, we defined how primary human fibroblasts respond to a panel of mitochondrial inhibitors to trigger adaptive stress responses. Using metabolomic and transcriptomic analyses, we established integrated signatures of mitochondrial stress. We developed a tool, stress quantification using integrated datasets (SQUID), to deconvolute mitochondrial stress signatures from existing datasets. Using SQUID, we profiled mitochondrial stress in The Cancer Genome Atlas (TCGA) PanCancer Atlas, identifying a signature of pyruvate import deficiency in IDH1-mutant glioma. Thus, this study defines a tool to identify specific mitochondrial stress signatures, which may be applied to a range of systems.

Keywords: CP: Metabolism; CP: Systems biology; cancer metabolism; integrated multi-omics; integrated stress response; metabolomics; mitochondria; mitochondrial stress response; mitochondrial unfolded protein response; stress signatures

DOI: https://doi.org/10.1016/j.crmeth.2025.101027

Nat Commun. 2025 Apr 17. 16(1): 3641

Coupling of ribosome biogenesis and translation initiation in human mitochondria.

Marleen Heinrichs, Anna Franziska Finke, Shintaro Aibara, Angelique Krempler, Angela Boshnakovska, Peter Rehling, Hauke S Hillen, Ricarda Richter-Dennerlein.

Biogenesis of mitoribosomes requires dedicated chaperones, RNA-modifying enzymes, and GTPases, and defects in mitoribosome assembly lead to severe mitochondriopathies in humans. Here, we characterize late-step assembly states of the small mitoribosomal subunit (mtSSU) by combining genetic perturbation and mutagenesis analysis with biochemical and structural approaches. Isolation of native mtSSU biogenesis intermediates via a FLAG-tagged variant of the GTPase MTG3 reveals three distinct assembly states, which show how factors cooperate to mature the 12S rRNA. In addition, we observe four distinct primed initiation mtSSU states with an incompletely matured rRNA, suggesting that biogenesis and translation initiation are not mutually exclusive processes but can occur simultaneously. Together, these results provide insights into mtSSU biogenesis and suggest a functional coupling between ribosome biogenesis and translation initiation in human mitochondria.

DOI: https://doi.org/10.1038/s41467-025-58827-x

Int J Mol Sci. 2025 Mar 28. pii: 3121. [Epub ahead of print]26(7):

The Proline Dehydrogenase Gene CsProDH1 Regulates Homeostasis of the Pro-P5C Cycle Under Drought Stress in Tea Plants.

Deng Deng, Qinqin Gao, Rou Zeng, Jie Jiang, Qiang Shen, Yuanchun Ma, Wanping Fang, Xujun Zhu.

The homeostasis of the proline-Δ1-pyrroline-5-carboxylate (Pro-P5C) cycle, mediated by proline dehydrogenase (ProDH), plays a critical role in plants in response to abiotic stresses. The biological function of gene CsProDH1 under drought stress and its effects on amino acid metabolism and photosynthesis through proline metabolism were investigated. Enzymatic characterization of the CsProDH1 protein was conducted in vitro. Overexpression of CsProDH1 aggravated plant stress, as evident by reduced photosynthetic efficiency and increased reactive oxygen species, which activated the Pro-P5C cycle. In contrast, silencing CsProDH1 enhanced plant drought resistance, increased proline accumulation, and protected photosynthesis. Studies indicate that exogenous amino acid application mitigates drought-induced physiological impairments in plants by maintaining cellular homeostasis, with particular efficacy observed in enhancing tea plant drought resilience through improved osmotic adjustment and antioxidant capacity. This study uncovers the significant role of CsProDH1 in plant drought resistance and its regulatory mechanism, offering potential gene targets and application strategies for enhancing crop drought resistance.

Keywords: Pro-P5C cycle; drought stress; proline dehydrogenase

DOI: https://doi.org/10.3390/ijms26073121

Bio Protoc. 2025 Apr 05. 15(7): e5257

Ex Vivo Measurement of Stable Isotope-Labeled Fatty Acid Incorporation Into Phospholipids in Isolated Mice Muscle.

Tomoki Sato, Shinji Miura.

With the advancement of liquid chromatography-mass spectrometry (LC-MS/MS), the quantification of glycerophospholipid (PL) molecules has become more accessible, leading to the discovery of numerous enzymes responsible for determining the acyl groups attached to these molecules. Metabolic tracer experiments using radioisotopes and stable isotopes are powerful tools for defining the function of metabolic enzymes and metabolic flux. We have established an ex vivo muscle experimental system using stable isotope-labeled fatty acids to evaluate fatty acid incorporation into PL molecules. Here, we describe a method to incorporate fatty acids with stable isotope labels into excised skeletal muscle and detect the PL molecules containing labeled acyl chains by LC-MS/MS. Key features • Quantify the metabolism of fatty acids into phospholipid acyl chains. • Enable measurements in excised muscle samples. • Assess the effects of genetic recombination of acyltransferases.

Keywords: Acyl chain; Free-fatty acid; Liquid chromatography–mass spectrometry; Phospholipid; Skeletal muscle; Stable isotope tracer

DOI: https://doi.org/10.21769/BioProtoc.5257