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Wai T. Is mitochondrial morphology important for cellular physiology? Trends Endocrinol Metab 2024:S1043-2760(24)00123-1. [PMID: 38866638 DOI: 10.1016/j.tem.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024]
Abstract
Mitochondria are double membrane-bound organelles the network morphology of which in cells is shaped by opposing events of fusion and fission executed by dynamin-like GTPases. Mutations in these genes can perturb the form and functions of mitochondria in cell and animal models of mitochondrial diseases. An expanding array of chemical, mechanical, and genetic stressors can converge on mitochondrial-shaping proteins and disrupt mitochondrial morphology. In recent years, studies aimed at disentangling the multiple roles of mitochondrial-shaping proteins beyond fission or fusion have provided insights into the homeostatic relevance of mitochondrial morphology. Here, I review the pleiotropy of mitochondrial fusion and fission proteins with the aim of understanding whether mitochondrial morphology is important for cell and tissue physiology.
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Affiliation(s)
- Timothy Wai
- Institut Pasteur, Mitochondrial Biology, CNRS UMR 3691, Université Paris Cité, Paris, France.
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Poulton NC, DeJesus MA, Munsamy-Govender V, Kanai M, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: The whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. Cell Chem Biol 2024; 31:669-682.e7. [PMID: 38266648 PMCID: PMC11031301 DOI: 10.1016/j.chembiol.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/13/2023] [Accepted: 12/23/2023] [Indexed: 01/26/2024]
Abstract
Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. The conserved whiB7 stress response reduces the effectiveness of antibiotic therapy by activating several intrinsic antibiotic resistance mechanisms. Despite our comprehensive biochemical understanding of WhiB7, the complex set of signals that induce whiB7 expression remain less clear. We employed a reporter-based, genome-wide CRISPRi epistasis screen to identify a diverse set of 150 mycobacterial genes whose inhibition results in constitutive whiB7 expression. We show that whiB7 expression is determined by the amino acid composition of the 5' regulatory uORF, thereby allowing whiB7 to sense amino acid starvation. Although deprivation of many amino acids can induce whiB7, whiB7 specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme, aspC. These findings describe a metabolic function for whiB7 and help explain its evolutionary conservation across mycobacterial species occupying diverse ecological niches.
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Affiliation(s)
- Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | | | - Mariko Kanai
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Karl Matthew Lin
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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Gorityala N, Baidya AS, Sagurthi SR. Genome mining of Mycobacterium tuberculosis: targeting SufD as a novel drug candidate through in silico characterization and inhibitor screening. Front Microbiol 2024; 15:1369645. [PMID: 38686111 PMCID: PMC11057465 DOI: 10.3389/fmicb.2024.1369645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Tuberculosis (TB) stands as the second most fatal infectious disease globally, causing 1.3 million deaths in 2022. The resurgence of TB and the alarming rise of antibiotic resistance demand urgent call to develop novel antituberculosis drugs. Despite concerted efforts to control TB, the disease persists and spreads rapidly on a global scale. Targeting stress response pathways in Mycobacterium tuberculosis (Mtb) has become imperative to achieve complete eradication. This study employs subtractive genomics to identify and prioritize potential drug targets among the hypothetical proteins of Mtb, focusing on indispensable pathways. Amongst 177 essential hypothetical proteins, 152 were nonhomologous to human. These proteins participated in 34 pathways, and a 20-fold enrichment of SUF pathway genes led to its selection as a target pathway. Fe-S clusters are fundamental, widely distributed protein cofactors involved in vital cellular processes. The survival of Mtb in a hypoxic environment relies on the iron-sulfur (Fe-S) cluster biogenesis pathway for the repair of damaged Fe-S clusters. It also protects pathogen against drugs, ensuring controlled iron utilization and contributing to drug resistance. In Mtb, six proteins of Fe-S cluster assembly pathway are encoded by the suf operon. The present study was focused on SufD because of its role in iron acquisition and prevention of Fenton reaction. The research further delves into the in silico characterization of SufD, utilizing bioinformatics tools for sequence and structure based analysis. The protein's structural features, including the identification of conserved regions, motifs, and 3D structure prediction enhanced functional annotation. Target based virtual screening of compounds from the ChEMBL database resulted in 12 inhibitors with best binding affinities. Drug likeness and ADMET profiling of potential inhibitors identified promising compounds with favorable drug-like properties. The study also involved cloning in SUMO-pRSF-Duet1 expression vector, overexpression, and purification of recombinant SufD from E. coli BL21 (DE3) cells. Optimization of expression conditions resulted in soluble production, and subsequent purification highlighting the efficacy of the SUMO fusion system for challenging Mtb proteins in E. coli. These findings provide valuable insights into pharmacological targets for future experimental studies, holding promise for the development of targeted therapy against Mtb.
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Affiliation(s)
- Neelima Gorityala
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Anthony Samit Baidya
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Someswar R Sagurthi
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
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Li YQ, An XL, Jin FY, Bai YF, Li T, Yang XY, Liu SP, Gao XM, Mao N, Xu H, Cai WC, Yang F. ISRIB inhibits the senescence of type II pulmonary epithelial cells to alleviate pulmonary fibrosis induced by silica in mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115410. [PMID: 37647802 DOI: 10.1016/j.ecoenv.2023.115410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
The role and mechanisms of integrated stress response inhibitor (ISRIB) on silicosis are still not well defined. In the present study, the effects of ISRIB on cellular senescence and pulmonary fibrosis in silicosis were evaluated by RNA sequencing, micro-computed tomography, pulmonary function assessment, histological examination, and Western blot analysis. The results showed that ISRIB significantly reduced the degree of pulmonary fibrosis in mice with silicosis and reduced the expression of type I collagen, fibronectin, α-smooth muscle actin, and transforming growth factor-β1. Both in vivo and in vitro results showed that ISRIB reversed the expression of senescence-related factors β-galactosidase, phosphor-ataxia telangiectasia mutated, phosphor-ataxia telangiectasia and Rad3-related protein, p-p53, p21, p16, and plasminogen activator inhibitor type 1. The aforementioned results were consistent with the sequencing results. These findings implied that ISRIB might reduce the degree of pulmonary fibrosis in mice with silicosis by inhibiting the cellular senescence of alveolar epithelial cell type II.
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Affiliation(s)
- Ya-Qian Li
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Xu-Liang An
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Fu-Yu Jin
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Yi-Fei Bai
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Tian Li
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Xin-Yu Yang
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Shu-Peng Liu
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Xue-Min Gao
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China; NHC Key Laboratory of Pneumoconiosis,Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Na Mao
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China
| | - Hong Xu
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China; Health Scicence Center, North China University of Science and Technology, Tangshan, China
| | - Wen-Chen Cai
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China.
| | - Fang Yang
- School of public and health, Hebei Key Laboratory for Organ Fibrosis Research, North China University of Science and Technology, Tangshan, China.
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Poulton NC, DeJesus MA, Munsamy-Govender V, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: the whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543512. [PMID: 37333137 PMCID: PMC10274678 DOI: 10.1101/2023.06.02.543512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. These bacteria are highly intrinsically drug resistant, making infections challenging to treat. The conserved whiB7 stress response is a key contributor to mycobacterial intrinsic drug resistance. Although we have a comprehensive structural and biochemical understanding of WhiB7, the complex set of signals that activate whiB7 expression remain less clear. It is believed that whiB7 expression is triggered by translational stalling in an upstream open reading frame (uORF) within the whiB7 5' leader, leading to antitermination and transcription into the downstream whiB7 ORF. To define the signals that activate whiB7, we employed a genome-wide CRISPRi epistasis screen and identified a diverse set of 150 mycobacterial genes whose inhibition results in constitutive whiB7 activation. Many of these genes encode amino acid biosynthetic enzymes, tRNAs, and tRNA synthetases, consistent with the proposed mechanism for whiB7 activation by translational stalling in the uORF. We show that the ability of the whiB7 5' regulatory region to sense amino acid starvation is determined by the coding sequence of the uORF. The uORF shows considerable sequence variation among different mycobacterial species, but it is universally and specifically enriched for alanine. Providing a potential rationalization for this enrichment, we find that while deprivation of many amino acids can activate whiB7 expression, whiB7 specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme, aspC. Our results provide a holistic understanding of the biological pathways that influence whiB7 activation and reveal an extended role for the whiB7 pathway in mycobacterial physiology, beyond its canonical function in antibiotic resistance. These results have important implications for the design of combination drug treatments to avoid whiB7 activation, as well as help explain the conservation of this stress response across a wide range of pathogenic and environmental mycobacteria.
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Affiliation(s)
- Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Vanisha Munsamy-Govender
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Cameron G Roberts
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Karl Matthew Lin
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
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