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Liu Y, Murphy K, Fernandes N, Moore RET, Pennisi I, Williams R, Rehkämper M, Larrouy-Maumus G. Transition metal homoeostasis is key to metabolism and drug tolerance of Mycobacterium abscessus. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:25. [PMID: 39359892 PMCID: PMC11442307 DOI: 10.1038/s44259-024-00042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 07/24/2024] [Indexed: 10/04/2024]
Abstract
Antimicrobial resistance (AMR) is one of the major challenges humans are facing this century. Understanding the mechanisms behind the rise of AMR is therefore crucial to tackling this global threat. The presence of transition metals is one of the growth-limiting factors for both environmental and pathogenic bacteria, and the mechanisms that bacteria use to adapt to and survive under transition metal toxicity resemble those correlated with the rise of AMR. A deeper understanding of transition metal toxicity and its potential as an antimicrobial agent will expand our knowledge of AMR and assist the development of therapeutic strategies. In this study, we investigate the antimicrobial effect of two transition metal ions, namely cobalt (Co2+) and nickel (Ni2+), on the non-tuberculous environmental mycobacterium and the opportunistic human pathogen Mycobacterium abscessus. The minimum inhibitory concentrations of Co2+ and Ni2+ on M. abscessus were first quantified and their impact on the bacterial intracellular metallome was investigated. A multi-omics strategy that combines transcriptomics, bioenergetics, metabolomics, and phenotypic assays was designed to further investigate the mechanisms behind the effects of transition metals. We show that transition metals induced growth defect and changes in transcriptome and carbon metabolism in M. abscessus, while the induction of the glyoxylate shunt and the WhiB7 regulon in response to metal stresses could be the key response that led to higher AMR levels. Meanwhile, transition metal treatment alters the bacterial response to clinically relevant antibiotics and enhances the uptake of clarithromycin into bacterial cells, leading to increased efficacy. This work provides insights into the tolerance mechanisms of M. abscessus to transition metal toxicity and demonstrates the possibility of using transition metals to adjuvant the efficacy of currently using antimicrobials against M. abscessus infections.
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Affiliation(s)
- Yi Liu
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Katy Murphy
- Department of Earth Science and Engineering, Royal School of Mines, Imperial College London, London, UK
| | - Nadia Fernandes
- Imperial BRC Genomics Faculty, Imperial College London, London, UK
| | - Rebekah E T Moore
- Department of Earth Science and Engineering, Royal School of Mines, Imperial College London, London, UK
| | - Ivana Pennisi
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Richard Williams
- Imperial BRC Genomics Faculty, Imperial College London, London, UK
| | - Mark Rehkämper
- Department of Earth Science and Engineering, Royal School of Mines, Imperial College London, London, UK
| | - Gerald Larrouy-Maumus
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
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Xu J, Ma S, Huang Y, Zhang Q, Huang L, Xu H, Suleiman IM, Li P, Wang Z, Xie J. Mycobacterium marinum MMAR_0267-regulated copper utilization facilitates bacterial escape from phagolysosome. Commun Biol 2024; 7:1180. [PMID: 39300168 DOI: 10.1038/s42003-024-06860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 09/06/2024] [Indexed: 09/22/2024] Open
Abstract
The host limits Mycobacterium tuberculosis (Mtb) by enriching copper in high concentrations. This research investigates how Mtb escapes copper stress. The membrane protein encoded by Mtb Rv0102, when its homolog in M. smegmatis (MSMEG_4702) was knocked out, resulted in a fourfold decrease in intracellular copper levels and enhanced tolerance to elevated extracellular copper concentrations. Similarly, knockout mutants of its homolog in M. marinum (MMAR_0267) showed increased virulence in zebrafish and higher bacterial load within macrophages. In THP-1 cells infected with MMAR_0267 deletion mutants, the intracellular survival of these mutants increased, along with reduced THP-1 cell apoptosis. Deficiency in copper down-regulated the transcriptional level of the virulence factor CFP-10 in M. marinum, suppressed cytosolic signaling via the macrophage STING pathway, leading to decreased production of IFN-β and reduced cell apoptosis. In conclusion, these findings highlight the significant impact of copper on the survival and reproduction of mycobacteria, underscoring the importance of studying mycobacterial adaptation mechanisms in copper-rich environments.
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Affiliation(s)
- Junqi Xu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shaying Ma
- Chongqing Public Health Medical Center, Chongqing, China
| | - Yu Huang
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Qiao Zhang
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Lingxi Huang
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Hongxiang Xu
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Ismail Mohamed Suleiman
- Chongqing Emergency Medical Center, Chongqing the Fourth Hospital, Jiankang Road, Yuzhong, Chongqing, 400014, China
| | - Peibo Li
- Chongqing Public Health Medical Center, Chongqing, China.
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing, 400715, China.
| | - Jianping Xie
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatic Science of Chongqing, Institute of Modern Biopharmaceuticals, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Chongqing Public Health Medical Center, Chongqing, China.
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Baruzzo G, Serafini A, Finotello F, Sanavia T, Cioetto-Mazzabò L, Boldrin F, Lavezzo E, Barzon L, Toppo S, Provvedi R, Manganelli R, Di Camillo B. Role of the Extracytoplasmic Function Sigma Factor SigE in the Stringent Response of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0294422. [PMID: 36946740 PMCID: PMC10100808 DOI: 10.1128/spectrum.02944-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/15/2023] [Indexed: 03/23/2023] Open
Abstract
Bacteria respond to nutrient starvation implementing the stringent response, a stress signaling system resulting in metabolic remodeling leading to decreased growth rate and energy requirements. A well-characterized model of stringent response in Mycobacterium tuberculosis is the one induced by growth in low phosphate. The extracytoplasmic function (ECF) sigma factor SigE was previously suggested as having a key role in the activation of stringent response. In this study, we challenge this hypothesis by analyzing the temporal dynamics of the transcriptional response of a sigE mutant and its wild-type parental strain to low phosphate using RNA sequencing. We found that both strains responded to low phosphate with a typical stringent response trait, including the downregulation of genes encoding ribosomal proteins and RNA polymerase. We also observed transcriptional changes that support the occurring of an energetics imbalance, compensated by a reduced activity of the electron transport chain, decreased export of protons, and a remodeling of central metabolism. The most striking difference between the two strains was the induction in the sigE mutant of several stress-related genes, in particular, the genes encoding the ECF sigma factor SigH and the transcriptional regulator WhiB6. Since both proteins respond to redox unbalances, their induction suggests that the sigE mutant is not able to maintain redox homeostasis in response to the energetics imbalance induced by low phosphate. In conclusion, our data suggest that SigE is not directly involved in initiating stringent response but in protecting the cell from stress consequent to the low phosphate exposure and activation of stringent response. IMPORTANCE Mycobacterium tuberculosis can enter a dormant state enabling it to establish latent infections and to become tolerant to antibacterial drugs. Dormant bacteria's physiology and the mechanism(s) used by bacteria to enter dormancy during infection are still unknown due to the lack of reliable animal models. However, several in vitro models, mimicking conditions encountered during infection, can reproduce different aspects of dormancy (growth arrest, metabolic slowdown, drug tolerance). The stringent response, a stress response program enabling bacteria to cope with nutrient starvation, is one of them. In this study, we provide evidence suggesting that the sigma factor SigE is not directly involved in the activation of stringent response as previously hypothesized, but it is important to help the bacteria to handle the metabolic stress related to the adaptation to low phosphate and activation of stringent response, thus giving an important contribution to our understanding of the mechanism behind stringent response development.
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Affiliation(s)
- Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padua, Italy
| | - Agnese Serafini
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Tiziana Sanavia
- Department of Information Engineering, University of Padova, Padua, Italy
| | | | - Francesca Boldrin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padua, Italy
- Department of Comparative Biomedicine and Food Science, University of Padova, Padua, Italy
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The polyHIS Tract of Yeast AMPK Coordinates Carbon Metabolism with Iron Availability. Int J Mol Sci 2023; 24:ijms24021368. [PMID: 36674878 PMCID: PMC9863760 DOI: 10.3390/ijms24021368] [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: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Energy status in all eukaryotic cells is sensed by AMP-kinases. We have previously found that the poly-histidine tract at the N-terminus of S. cerevisiae AMPK (Snf1) inhibits its function in the presence of glucose via a pH-regulated mechanism. We show here that in the absence of glucose, the poly-histidine tract has a second function, linking together carbon and iron metabolism. Under conditions of iron deprivation, when different iron-intense cellular systems compete for this scarce resource, Snf1 is inhibited. The inhibition is via an interaction of the poly-histidine tract with the low-iron transcription factor Aft1. Aft1 inhibition of Snf1 occurs in the nucleus at the nuclear membrane, and only inhibits nuclear Snf1, without affecting cytosolic Snf1 activities. Thus, the temporal and spatial regulation of Snf1 activity enables a differential response to iron depending upon the type of carbon source. The linkage of nuclear Snf1 activity to iron sufficiency ensures that sufficient clusters are available to support respiratory enzymatic activity and tests mitochondrial competency prior to activation of nuclear Snf1.
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Djoko K, Cavet J. Perspectives on Metals in Microbiology. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35786425 DOI: 10.1099/mic.0.001215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Karrera Djoko
- Department of Biosciences, Durham University, Durham, UK
| | - Jennifer Cavet
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
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Beste DJV. New perspectives on an ancient pathogen: thoughts for World Tuberculosis Day 2022. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35357305 PMCID: PMC9558351 DOI: 10.1099/mic.0.001178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dany J V Beste
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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Thomas GH. Microbial Musings – June 2021. Microbiology (Reading) 2021; 167. [DOI: 10.1099/mic.0.001077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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