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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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Chen YS, Gehring K. New insights into the structure and function of CNNM proteins. FEBS J 2023; 290:5475-5495. [PMID: 37222397 DOI: 10.1111/febs.16872] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 05/23/2023] [Indexed: 05/25/2023]
Abstract
Magnesium (Mg2+ ) is the most abundant divalent cation in cells and plays key roles in almost all biological processes. CBS-pair domain divalent metal cation transport mediators (CNNMs) are a newly characterized class of Mg2+ transporters present throughout biology. Originally discovered in bacteria, there are four CNNM proteins in humans, which are involved in divalent cation transport, genetic diseases, and cancer. Eukaryotic CNNMs are composed of four domains: an extracellular domain, a transmembrane domain, a cystathionine-β-synthase (CBS)-pair domain, and a cyclic nucleotide-binding homology domain. The transmembrane and CBS-pair core are the defining features of CNNM proteins with over 20 000 protein sequences known from over 8000 species. Here, we review the structural and functional studies of eukaryotic and prokaryotic CNNMs that underlie our understanding of their regulation and mechanism of ion transport. Recent structures of prokaryotic CNNMs confirm the transmembrane domain mediates ion transport with the CBS-pair domain likely playing a regulatory role through binding divalent cations. Studies of mammalian CNNMs have identified new binding partners. These advances are driving progress in understanding this deeply conserved and widespread family of ion transporters.
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Affiliation(s)
- Yu Seby Chen
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Kalle Gehring
- Department of Biochemistry & Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
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3
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Metaane S, Monteil V, Douché T, Giai Gianetto Q, Matondo M, Maufrais C, Norel F. Loss of CorA, the primary magnesium transporter of Salmonella, is alleviated by MgtA and PhoP-dependent compensatory mechanisms. PLoS One 2023; 18:e0291736. [PMID: 37713445 PMCID: PMC10503707 DOI: 10.1371/journal.pone.0291736] [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: 06/09/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of stationary phase cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have recently shown that a ΔrpoS mutation decreases the magnesium content and expression level of the housekeeping Mg2+-transporter CorA in stationary phase Salmonella. The other two Mg2+-transporters of Salmonella are encoded by the PhoP-activated mgtA and mgtB genes and are expressed under magnesium starvation. The σS control of corA prompted us to evaluate the impact of CorA in stationary phase Salmonella cells, by using global and analytical proteomic analyses and physiological assays. The ΔcorA mutation conferred a competitive disadvantage to exit from stationary phase, and slightly impaired motility, but had no effect on total and free cellular magnesium contents. In contrast to the wild-type strain, the ΔcorA mutant produced MgtA, but not MgtB, in the presence of high extracellular magnesium concentration. Under these conditions, MgtA production in the ΔcorA mutant did not require PhoP. Consistently, a ΔmgtA, but not a ΔphoP, mutation slightly reduced the magnesium content of the ΔcorA mutant. Synthetic phenotypes were observed when the ΔphoP and ΔcorA mutations were combined, including a strong reduction in growth and motility, independently of the extracellular magnesium concentration. The abundance of several proteins involved in flagella formation, chemotaxis and secretion was lowered by the ΔcorA and ΔphoP mutations in combination, but not alone. These findings unravel the importance of PhoP-dependent functions in the absence of CorA when magnesium is sufficient. Altogether, our data pinpoint a regulatory network, where the absence of CorA is sensed by the cell and compensated by MgtA and PhoP- dependent mechanisms.
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Affiliation(s)
- Selma Metaane
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Véronique Monteil
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
| | - Thibaut Douché
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Quentin Giai Gianetto
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Mariette Matondo
- Proteomic Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS UAR 2024, Université Paris Cité, Paris, France
| | - Corinne Maufrais
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Françoise Norel
- Biochimie des Interactions Macromoléculaires, Institut Pasteur, CNRS UMR3528, Université Paris Cité, Paris, France
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4
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Wang J, Sheng Z, Liu Y, Chen X, Wang S, Yang H. Combined proteomic and transcriptomic analysis of the antimicrobial mechanism of tannic acid against Staphylococcus aureus. Front Pharmacol 2023; 14:1178177. [PMID: 37654613 PMCID: PMC10466393 DOI: 10.3389/fphar.2023.1178177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023] Open
Abstract
Staphylococcus aureus is a zoonotic opportunistic pathogen that represents a significant threat to public health. Previous studies have shown that tannic acid (TA) has an inhibitory effect on a variety of bacteria. In this study, the proteome and transcriptome of S. aureus were analyzed to comprehensively assess changes in genes and proteins induced by TA. Initial observations of morphological changes revealed that TA damaged the integrity of the cell membrane. Next, proteomic and genetic analyses showed that exposure to TA altered the expression levels of 651 differentially expressed proteins (DEPs, 283 upregulated and 368 downregulated) and 503 differentially expressed genes (DEGs, 191 upregulated and 312 downregulated). Analysis of the identified DEPs and DEGs suggested that TA damages the integrity of the cell envelope by decreasing the expression and protein abundance of enzymes involved in the synthesis of peptidoglycans, teichoic acids and fatty acids, such as murB, murQ, murG, fmhX and tagA. After treatment with TA, the assembly of ribosomes in S. aureus was severely impaired by significant reductions in available ribosome components, and thus protein synthesis was hindered. The levels of genes and proteins associated with amino acids and purine synthesis were remarkably decreased, which further reduced bacterial viability. In addition, ABC transporters, which are involved in amino acid and ion transport, were also badly affected. Our results reveal the molecular mechanisms underlying the effects of TA on S. aureus and provide a theoretical basis for the application of TA as an antibacterial chemotherapeutic agent.
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Affiliation(s)
- Jing Wang
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, Jiangsu Province, China
| | - Zhicun Sheng
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, Jiangsu Province, China
| | - Yunying Liu
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, Jiangsu Province, China
- Zhongchong Sino Biotech Taizhou Co., Ltd., Taizhou, Jiangsu Province, China
| | - Xiaolan Chen
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, Jiangsu Province, China
| | - Shuaibing Wang
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, Jiangsu Province, China
| | - Haifeng Yang
- Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, Jiangsu Province, China
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5
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Ishida Y, Zhang C, Satoh K, Ito M. Physiological importance and role of Mg 2+ in improving bacterial resistance to cesium. Front Microbiol 2023; 14:1201121. [PMID: 37415808 PMCID: PMC10321302 DOI: 10.3389/fmicb.2023.1201121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
Cesium (Cs) is an alkali metal with radioactive isotopes such as 137Cs and 134Cs. 137Cs, a product of uranium fission, has garnered attention as a radioactive contaminant. Radioactive contamination remediation using microorganisms has been the focus of numerous studies. We investigated the mechanism underlying Cs+ resistance in Microbacterium sp. TS-1 and other representative microorganisms, including Bacillus subtilis. The addition of Mg2+ effectively improved the Cs+ resistance of these microorganisms. When exposed to high concentrations of Cs+, the ribosomes of Cs+-sensitive mutants of TS-1 collapsed. Growth inhibition of B. subtilis in a high-concentration Cs+ environment was because of a drastic decrease in the intracellular potassium ion concentration and not the destabilization of the ribosomal complex. This is the first study demonstrating that the toxic effect of Cs+ on bacterial cells differs based on the presence of a Cs+ efflux mechanism. These results will aid in utilizing high-concentration Cs+-resistant microorganisms for radioactive contamination remediation in the future.
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Affiliation(s)
- Yoshiki Ishida
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Chongkai Zhang
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Katsuya Satoh
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Takasaki, Gunma, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
- Bio-Resilience Research Project (BRRP), Toyo University, Oura-gun, Gunma, Japan
- Bio Nano Electronics Research Centre, Toyo University, Kawagoe, Saitama, Japan
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Yu T, Jiang J, Yu Q, Li X, Zeng F. Structural Insights into the Distortion of the Ribosomal Small Subunit at Different Magnesium Concentrations. Biomolecules 2023; 13:biom13030566. [PMID: 36979501 PMCID: PMC10046523 DOI: 10.3390/biom13030566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Magnesium ions are abundant and play indispensable functions in the ribosome. A decrease in Mg2+ concentration causes 70S ribosome dissociation and subsequent unfolding. Structural distortion at low Mg2+ concentrations has been observed in an immature pre50S, while the structural changes in mature subunits have not yet been studied. Here, we purified the 30S subunits of E. coli cells under various Mg2+ concentrations and analyzed their structural distortion by cryo-electron microscopy. Upon systematically interrogating the structural heterogeneity within the 1 mM Mg2+ dataset, we observed 30S particles with different levels of structural distortion in the decoding center, h17, and the 30S head. Our model showed that, when the Mg2+ concentration decreases, the decoding center distorts, starting from h44 and followed by the shifting of h18 and h27, as well as the dissociation of ribosomal protein S12. Mg2+ deficiency also eliminates the interactions between h17, h10, h15, and S16, resulting in the movement of h17 towards the tip of h6. More flexible structures were observed in the 30S head and platform, showing high variability in these regions. In summary, the structures resolved here showed several prominent distortion events in the decoding center and h17. The requirement for Mg2+ in ribosomes suggests that the conformational changes reported here are likely shared due to a lack of cellular Mg2+ in all domains of life.
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Affiliation(s)
- Ting Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Junyi Jiang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Qianxi Yu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Xin Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
| | - Fuxing Zeng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, No. 1088 Xueyuan Avenue, Shenzhen 518055, China
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7
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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8
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Abstract
By chance, we discovered a window of extracellular magnesium (Mg2+) availability that modulates the division frequency of Bacillus subtilis without affecting its growth rate. In this window, cells grown with excess Mg2+ produce shorter cells than do those grown in unsupplemented medium. The Mg2+-responsive adjustment in cell length occurs in both rich and minimal media as well as in domesticated and undomesticated strains. Of other divalent cations tested, manganese (Mn2+) and zinc (Zn2+) also resulted in cell shortening, but this occurred only at concentrations that affected growth. Cell length decreased proportionally with increasing Mg2+ from 0.2 mM to 4.0 mM, with little or no detectable change being observed in labile, intracellular Mg2+, based on a riboswitch reporter. Cells grown in excess Mg2+ had fewer nucleoids and possessed more FtsZ-rings per unit cell length, consistent with the increased division frequency. Remarkably, when shifting cells from unsupplemented to supplemented medium, more than half of the cell length decrease occurred in the first 10 min, consistent with rapid division onset. Relative to unsupplemented cells, cells growing at steady-state with excess Mg2+ showed an enhanced expression of a large number of SigB-regulated genes and the activation of the Fur, MntR, and Zur regulons. Thus, by manipulating the availability of one nutrient, we were able to uncouple the growth rate from the division frequency and identify transcriptional changes that suggest that cell division is accompanied by the general stress response and an enhanced demand to sequester and/or increase the uptake of iron, Mn2+, and Zn2+. IMPORTANCE The signals that cells use to trigger cell division are unknown. Although division is often considered intrinsic to the cell cycle, microorganisms can continue to grow and repeat rounds of DNA replication without dividing, indicating that cycles of division can be skipped. Here, we show that by manipulating a single nutrient, namely, Mg2+, cell division can be uncoupled from the growth rate. This finding can be applied to investigate the nature of the cell division signal(s).
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Ishida Y, Koretsune T, Ishiuchi E, Teshima M, Ito M. A magnesium transporter is involved in the cesium ion resistance of the high-concentration cesium ion-resistant bacterium Microbacterium sp. TS-1. Front Microbiol 2023; 14:1136514. [PMID: 36910217 PMCID: PMC9995610 DOI: 10.3389/fmicb.2023.1136514] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 02/25/2023] Open
Abstract
Cesium ion (Cs+) resistance has been reported in bacteria but is poorly understood as reports on Cs+-resistant bacteria have been limited. We previously reported a novel Cs+/H+ antiporter CshA implicated in Cs+-resistance in Microbacterium sp. TS-1. The present study used the same screening method to isolate novel Cs+-sensitive mutants and their revertants from TS-1. A comparative mutation site analysis using whole-genome sequencing revealed that MTS1_03028 encodes the Mg2+ transporter MgtE and is a candidate Cs+ resistance-related gene. We performed a bioinformatic analysis of MTS1_03028 and complementation experiments on Cs+ resistance in the TS-1 MTS1_03028 mutants Mut5 and Mut7 as well as Escherichia coli expressing MTS1_03028 in the presence of Mg2+. We established the role of MgtE in Cs+ resistance through a functional analysis of TS-1. Enhancing Mg2+ transport by expression of MTS_03028 conferred increased Cs+ resistance. When this strain was exposed to Cs+ concentrations exceeding 200 mM, CshA consistently lowered the intracellular Cs+ concentration. To our knowledge, the present study is the first to clarify the mechanism of Cs+ resistance in certain bacteria. The study findings offer important insights into the mechanism of bacterial resistance to excess Cs+ in the environment, suggesting the potential for bioremediation in high Cs-contaminated areas.
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Affiliation(s)
- Yoshiki Ishida
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Takahiro Koretsune
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Eri Ishiuchi
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Miyu Teshima
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma, Japan.,Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, Japan.,Bio-Nano Electronics Research Center, Toyo University, Kawagoe, Saitama, Japan.,Bio-Resilience Research Project (BRRP), Toyo University, Oura-gun, Gunma, Japan
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10
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Jin F, Huang Y, Hattori M. Recent Advances in the Structural Biology of Mg 2+ Channels and Transporters. J Mol Biol 2022; 434:167729. [PMID: 35841930 DOI: 10.1016/j.jmb.2022.167729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 10/17/2022]
Abstract
Magnesium ions (Mg2+) are the most abundant divalent cations in living organisms and are essential for various physiological processes, including ATP utilization and the catalytic activity of numerous enzymes. Therefore, the homeostatic mechanisms associated with cellular Mg2+ are crucial for both eukaryotic and prokaryotic organisms and are thus strictly controlled by Mg2+ channels and transporters. Technological advances in structural biology, such as the expression screening of membrane proteins, in meso phase crystallization, and recent cryo-EM techniques, have enabled the structure determination of numerous Mg2+ channels and transporters. In this review article, we provide an overview of the families of Mg2+ channels and transporters (MgtE/SLC41, TRPM6/7, CorA/Mrs2, CorC/CNNM), and discuss the structural biology prospects based on the known structures of MgtE, TRPM7, CorA and CorC.
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Affiliation(s)
- Fei Jin
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yichen Huang
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China.
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The stress sigma factor σS/RpoS counteracts Fur repression of genes involved in iron and manganese metabolism and modulates the ionome of Salmonella enterica serovar Typhimurium. PLoS One 2022; 17:e0265511. [PMID: 35358211 PMCID: PMC8970401 DOI: 10.1371/journal.pone.0265511] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of quiescent cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen Salmonella enterica serovar Typhimurium, σS is also required for biofilm formation and virulence. We have previously identified sRNAs genes positively controlled by σS in Salmonella, including the two paralogous sRNA genes, ryhB1 and ryhB2/isrE. Expression of ryhB1 and ryhB2 is repressed by the ferric uptake regulator Fur when iron is available. In this study, we show that σS alleviates Fur-mediated repression of the ryhB genes and of additional Fur target genes. Moreover, σS induces transcription of the manganese transporter genes mntH and sitABCD and prevents their repression, not only by Fur, but also by the manganese-responsive regulator MntR. These findings prompted us to evaluate the impact of a ΔrpoS mutation on the Salmonella ionome. Inductively coupled plasma mass spectrometry analyses revealed a significant effect of the ΔrpoS mutation on the cellular concentration of manganese, magnesium, cobalt and potassium. In addition, transcriptional fusions in several genes involved in the transport of these ions were regulated by σS. This study suggests that σS controls fluxes of ions that might be important for the fitness of quiescent cells. Consistent with this hypothesis, the ΔrpoS mutation extended the lag phase of Salmonella grown in rich medium supplemented with the metal ion chelator EDTA, and this effect was abolished when magnesium, but not manganese or iron, was added back. These findings unravel the importance of σS and magnesium in the regrowth potential of quiescent cells.
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12
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Wendel BM, Pi H, Krüger L, Herzberg C, Stülke J, Helmann JD. A Central Role for Magnesium Homeostasis during Adaptation to Osmotic Stress. mBio 2022; 13:e0009222. [PMID: 35164567 PMCID: PMC8844918 DOI: 10.1128/mbio.00092-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
Osmotic stress is a significant physical challenge for free-living cells. Cells from all three domains of life maintain viability during osmotic stress by tightly regulating the major cellular osmolyte potassium (K+) and by import or synthesis of compatible solutes. It has been widely established that in response to high salt stress, many bacteria transiently accumulate high levels of K+, leading to bacteriostasis, with growth resuming only when compatible solutes accumulate and K+ levels are restored to biocompatible levels. Using Bacillus subtilis as a model system, we provide evidence that K+ fluxes perturb Mg2+ homeostasis: import of K+ upon osmotic upshift is correlated with Mg2+ efflux, and Mg2+ reimport is critical for adaptation. The transient growth inhibition resulting from hyperosmotic stress is coincident with loss of Mg2+ and a decrease in protein translation. Conversely, the reimport of Mg2+ is a limiting factor during resumption of growth. Furthermore, we show the essential signaling dinucleotide cyclic di-AMP fluctuates dynamically in coordination with Mg2+ and K+ levels, consistent with the proposal that cyclic di-AMP orchestrates the cellular response to osmotic stress. IMPORTANCE Environments with high concentrations of salt or other solutes impose an osmotic stress on cells, ultimately limiting viability by dehydration of the cytosol. A very common cellular response to high osmolarity is to immediately import high levels of potassium ion (K+), which helps prevent dehydration and allows time for the import or synthesis of biocompatible solutes that allow a resumption of growth. Here, using Bacillus subtilis as a model, we demonstrate that concomitant with K+ import there is a large reduction in intracellular magnesium (Mg2+) mediated by specific efflux pumps. Further, it is the reimport of Mg2+ that is rate-limiting for the resumption of growth. These coordinated fluxes of K+ and Mg2+ are orchestrated by cyclic-di-AMP, an essential second messenger in Firmicutes. These findings amend the conventional model for osmoadaptation and reveal that Mg2+ limitation is the proximal cause of the bacteriostasis that precedes resumption of growth.
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Affiliation(s)
- Brian M. Wendel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Hualiang Pi
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Larissa Krüger
- Department of General Microbiology, GZMB, Georg August University, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, GZMB, Georg August University, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg August University, Göttingen, Germany
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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13
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Raisman JC, Fiore MA, Tomin L, Adjei JKO, Aswad VX, Chu J, Domondon CJ, Donahue BA, Masciotti CA, McGrath CG, Melita J, Podbielski PA, Schreiner MR, Trumpore LJ, Wengert PC, Wrightstone EA, Hudson AO, Wadsworth CB. Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications. PLoS One 2022; 17:e0262370. [PMID: 35025928 PMCID: PMC8758062 DOI: 10.1371/journal.pone.0262370] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 11/19/2022] Open
Abstract
Neisseria commensals are an indisputable source of resistance for their pathogenic relatives. However, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage in vitro selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≥ 2 μg/mL) in the Neisseria commensal, N. elongata. Across multiple lineages (n = 7/16), we find mutations that reduce susceptibility to azithromycin converge on the locus encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC) through short tandem duplication events. Interestingly, one of the laboratory evolved mutations in rpmH is identical (7LKRTYQ12), and two nearly identical, to those recently reported to contribute to high-level azithromycin resistance in N. gonorrhoeae. Transformations into the ancestral N. elongata lineage confirmed the causality of both rpmH and rpsC mutations. Though most lineages inheriting duplications suffered in vitro fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Ultimately, studies like this will be critical for predicting commensal alleles that could rapidly disseminate into pathogen populations via allelic exchange across recombinogenic microbial genera.
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Affiliation(s)
- Jordan C. Raisman
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Michael A. Fiore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lucille Tomin
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Joseph K. O. Adjei
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Virginia X. Aswad
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jonathan Chu
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Christina J. Domondon
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Ben A. Donahue
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Claudia A. Masciotti
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Connor G. McGrath
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jo Melita
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Paul A. Podbielski
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Madelyn R. Schreiner
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lauren J. Trumpore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Peter C. Wengert
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Emalee A. Wrightstone
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Crista B. Wadsworth
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
- * E-mail:
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14
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Abstract
Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5' leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.
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Affiliation(s)
- Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA; .,Yale Microbial Sciences Institute, West Haven, Connecticut 06516, USA
| | - Carissa Chan
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, USA;
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15
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Abstract
CNNM/CorB proteins are a broadly conserved family of integral membrane proteins with close to 90,000 protein sequences known. They are associated with Mg2+ transport but it is not known if they mediate transport themselves or regulate other transporters. Here, we determine the crystal structure of an archaeal CorB protein in two conformations (apo and Mg2+-ATP bound). The transmembrane DUF21 domain exists in an inward-facing conformation with a Mg2+ ion coordinated by a conserved π-helix. In the absence of Mg2+-ATP, the CBS-pair domain adopts an elongated dimeric configuration with previously unobserved domain-domain contacts. Hydrogen-deuterium exchange mass spectrometry, analytical ultracentrifugation, and molecular dynamics experiments support a role of the structural rearrangements in mediating Mg2+-ATP sensing. Lastly, we use an in vitro, liposome-based assay to demonstrate direct Mg2+ transport by CorB proteins. These structural and functional insights provide a framework for understanding function of CNNMs in Mg2+ transport and associated diseases.
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16
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Nikolaeva DD, Gelfand MS, Garushyants SK. Simplification of Ribosomes in Bacteria with Tiny Genomes. Mol Biol Evol 2021; 38:58-66. [PMID: 32681797 PMCID: PMC7782861 DOI: 10.1093/molbev/msaa184] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
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Affiliation(s)
- Daria D Nikolaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
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17
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Galera-Laporta L, Comerci CJ, Garcia-Ojalvo J, Süel GM. IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria. Cell Syst 2021; 12:497-508. [PMID: 34139162 PMCID: PMC8570674 DOI: 10.1016/j.cels.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
Metal ions are essential for life and represent the second most abundant constituent (after water) of any living cell. While the biological importance of inorganic ions has been appreciated for over a century, we are far from a comprehensive understanding of the functional roles that ions play in cells and organisms. In particular, recent advances are challenging the traditional view that cells maintain constant levels of ion concentrations (ion homeostasis). In fact, the ionic composition (metallome) of cells appears to be purposefully dynamic. The scientific journey that started over 60 years ago with the seminal work by Hodgkin and Huxley on action potentials in neurons is far from reaching its end. New evidence is uncovering how changes in ionic composition regulate unexpected cellular functions and physiology, especially in bacteria, thereby hinting at the evolutionary origins of the dynamic metallome. It is an exciting time for this field of biology, which we discuss and refer to here as IonoBiology.
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Affiliation(s)
- Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colin J Comerci
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093- 0380, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093-0380, USA.
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18
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Abstract
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.
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19
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Huang Y, Mu K, Teng X, Zhao Y, Funato Y, Miki H, Zhu W, Xu Z, Hattori M. Identification and mechanistic analysis of an inhibitor of the CorC Mg 2+ transporter. iScience 2021; 24:102370. [PMID: 33912817 PMCID: PMC8066426 DOI: 10.1016/j.isci.2021.102370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/17/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022] Open
Abstract
The CorC/CNNM family of Na+-dependent Mg2+ transporters is ubiquitously conserved from bacteria to humans. CorC, the bacterial CorC/CNNM family of proteins, is involved in resistance to antibiotic exposure and in the survival of pathogenic microorganisms in their host environment. The CorC/CNNM family proteins possess a cytoplasmic region containing the regulatory ATP-binding site. CorC and CNNM have attracted interest as therapeutic targets, whereas inhibitors targeting the ATP-binding site have not been identified. Here, we performed a virtual screening of CorC by targeting its ATP-binding site, identified a compound named IGN95a with inhibitory effects on ATP binding and Mg2+ export, and determined the cytoplasmic domain structure in complex with IGN95a. Furthermore, a chemical cross-linking experiment indicated that with ATP bound to the cytoplasmic domain, the conformational equilibrium of CorC was shifted more toward the inward-facing state of the transmembrane domain. In contrast, IGN95a did not induce such a shift.
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Affiliation(s)
- Yichen Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Kaijie Mu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong New Area, Shanghai, 201203, China
| | - Xinyu Teng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yimeng Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong New Area, Shanghai, 201203, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong New Area, Shanghai, 201203, China
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
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20
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Akanuma G. Diverse relationships between metal ions and the ribosome. Biosci Biotechnol Biochem 2021; 85:1582-1593. [PMID: 33877305 DOI: 10.1093/bbb/zbab070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/30/2021] [Indexed: 11/12/2022]
Abstract
The ribosome requires metal ions for structural stability and translational activity. These metal ions are important for stabilizing the secondary structure of ribosomal RNA, binding of ribosomal proteins to the ribosome, and for interaction of ribosomal subunits. In this review, various relationships between ribosomes and metal ions, especially Mg2+ and Zn2+, are presented. Mg2+ regulates gene expression by modulating the translational stability and synthesis of ribosomes, which in turn contribute to the cellular homeostasis of Mg2+. In addition, Mg2+ can partly complement the function of ribosomal proteins. Conversely, a reduction in the cellular concentration of Zn2+ induces replacement of ribosomal proteins, which mobilizes free-Zn2+ in the cell and represses translation activity. Evolutional relationships between these metal ions and the ribosome are also discussed.
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Affiliation(s)
- Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan.,Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
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21
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Huang Y, Jin F, Funato Y, Xu Z, Zhu W, Wang J, Sun M, Zhao Y, Yu Y, Miki H, Hattori M. Structural basis for the Mg 2+ recognition and regulation of the CorC Mg 2+ transporter. SCIENCE ADVANCES 2021; 7:7/7/eabe6140. [PMID: 33568487 PMCID: PMC7875539 DOI: 10.1126/sciadv.abe6140] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/23/2020] [Indexed: 05/05/2023]
Abstract
The CNNM/CorC family proteins are Mg2+ transporters that are widely distributed in all domains of life. In bacteria, CorC has been implicated in the survival of pathogenic microorganisms. In humans, CNNM proteins are involved in various biological events, such as body absorption/reabsorption of Mg2+ and genetic disorders. Here, we determined the crystal structure of the Mg2+-bound CorC TM domain dimer. Each protomer has a single Mg2+ binding site with a fully dehydrated Mg2+ ion. The residues at the Mg2+ binding site are strictly conserved in both human CNNM2 and CNNM4, and many of these residues are associated with genetic diseases. Furthermore, we determined the structures of the CorC cytoplasmic region containing its regulatory ATP-binding domain. A combination of structural and functional analyses not only revealed the potential interface between the TM and cytoplasmic domains but also showed that ATP binding is important for the Mg2+ export activity of CorC.
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Affiliation(s)
- Yichen Huang
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Fei Jin
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research and Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong New Area, Shanghai 201203, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research and Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong New Area, Shanghai 201203, China
| | - Jing Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Medical Building, Room 128, 639 Long-Mian Road, Nanjing 200098, China
| | - Minxuan Sun
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Yimeng Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China
| | - Ye Yu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Medical Building, Room 128, 639 Long-Mian Road, Nanjing 200098, China
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Bioactive Small Molecules, Collaborative Innovation Center of Genetics and Development, and Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 2005 Songhu Road, Yangpu District, Shanghai 200438, China.
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22
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Dutagaci B, Nawrocki G, Goodluck J, Ashkarran AA, Hoogstraten CG, Lapidus LJ, Feig M. Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments. eLife 2021; 10:64004. [PMID: 33496264 PMCID: PMC7877912 DOI: 10.7554/elife.64004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Phase separation processes are increasingly being recognized as important organizing mechanisms of biological macromolecules in cellular environments. Well-established drivers of phase separation are multi-valency and intrinsic disorder. Here, we show that globular macromolecules may condense simply based on electrostatic complementarity. More specifically, phase separation of mixtures between RNA and positively charged proteins is described from a combination of multiscale computer simulations with microscopy and spectroscopy experiments. Phase diagrams were mapped out as a function of molecular concentrations in experiment and as a function of molecular size and temperature via simulations. The resulting condensates were found to retain at least some degree of internal dynamics varying as a function of the molecular composition. The results suggest a more general principle for phase separation that is based primarily on electrostatic complementarity without invoking polymer properties as in most previous studies. Simulation results furthermore suggest that such phase separation may occur widely in heterogenous cellular environment between nucleic acid and protein components.
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Affiliation(s)
- Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Joyce Goodluck
- Department of Physics, Michigan State University, East Lansing, United States
| | - Ali Akbar Ashkarran
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, United States
| | - Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Lisa J Lapidus
- Department of Physics, Michigan State University, East Lansing, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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23
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Nikolaeva DD, Gelfand MS, Garushyants SK. Simplification of Ribosomes in Bacteria with Tiny Genomes. Mol Biol Evol 2021. [PMID: 32681797 DOI: 10.1101/755876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (<1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We have identified the set of frequently lost ribosomal proteins and demonstrated that they tend to be positioned on the ribosome surface and have fewer contacts to other ribosome components. Moreover, some proteins are lost in an evolutionary correlated manner. The reduction of ribosomal RNA is also common, with deletions mostly occurring in free loops. Finally, the loss of the anti-Shine-Dalgarno sequence is associated with the loss of a higher number of ribosomal proteins.
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Affiliation(s)
- Daria D Nikolaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofya K Garushyants
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia
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24
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Yousuf S, Karlinsey JE, Neville SL, McDevitt CA, Libby SJ, Fang FC, Frawley ER. Manganese import protects Salmonella enterica serovar Typhimurium against nitrosative stress. Metallomics 2020; 12:1791-1801. [PMID: 33078811 DOI: 10.1039/d0mt00178c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Nitric oxide (NO˙) is a radical molecule produced by mammalian phagocytic cells as part of the innate immune response to bacterial pathogens. It exerts its antimicrobial activity in part by impairing the function of metalloproteins, particularly those containing iron and zinc cofactors. The pathogenic Gram-negative bacterium Salmonella enterica serovar typhimurium undergoes dynamic changes in its cellular content of the four most common metal cofactors following exposure to NO˙ stress. Zinc, iron and magnesium all decrease in response to NO˙ while cellular manganese increases significantly. Manganese acquisition is driven primarily by increased expression of the mntH and sitABCD transporters following derepression of MntR and Fur. ZupT also contributes to manganese acquisition in response to nitrosative stress. S. Typhimurium mutants lacking manganese importers are more sensitive to NO˙, indicating that manganese is important for resistance to nitrosative stress.
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Affiliation(s)
- Shehla Yousuf
- Rhodes College Biology Department, 2000 North Parkway, Memphis, TN 38112, USA.
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25
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Spice AJ, Aw R, Bracewell DG, Polizzi KM. Improving the reaction mix of a Pichia pastoris cell-free system using a design of experiments approach to minimise experimental effort. Synth Syst Biotechnol 2020; 5:137-144. [PMID: 32637667 PMCID: PMC7320237 DOI: 10.1016/j.synbio.2020.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022] Open
Abstract
A renaissance in cell-free protein synthesis (CFPS) is underway, enabled by the acceleration and adoption of synthetic biology methods. CFPS has emerged as a powerful platform technology for synthetic gene network design, biosensing and on-demand biomanufacturing. Whilst primarily of bacterial origin, cell-free extracts derived from a variety of host organisms have been explored, aiming to capitalise on cellular diversity and the advantageous properties associated with those organisms. However, cell-free extracts produced from eukaryotes are often overlooked due to their relatively low yields, despite the potential for improved protein folding and posttranslational modifications. Here we describe further development of a Pichia pastoris cell-free platform, a widely used expression host in both academia and the biopharmaceutical industry. Using a minimised Design of Experiments (DOE) approach, we were able to increase the productivity of the system by improving the composition of the complex reaction mixture. This was achieved in a minimal number of experimental runs, within the constraints of the design and without the need for liquid-handling robots. In doing so, we were able to estimate the main effects impacting productivity in the system and increased the protein synthesis of firefly luciferase and the biopharmaceutical HSA by 4.8-fold and 3.5-fold, respectively. This study highlights the P. pastoris-based cell-free system as a highly productive eukaryotic platform and displays the value of minimised DOE designs.
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Key Words
- AB, Albumin Blue
- CFPS, cell-free protein synthesis
- CHO, Chinese hamster ovary cells
- Cell-free protein synthesis
- DOE, design of Experiments
- DSD, definitive screening design
- Design of experiments (DOE)
- HSA, human serum albumin
- IRES, internal ribosome entry site
- Pichia pastoris
- RRL, rabbit reticulocyte lysate
- Synthetic biology
- VLP, virus-like particles
- WGE, wheat-germ etract
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Affiliation(s)
- Alex J. Spice
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Rochelle Aw
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Daniel G. Bracewell
- Department of Biochemical Engineering, University College London, London, UK
| | - Karen M. Polizzi
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, UK
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Ogura T, Kobayashi NI, Hermans C, Ichihashi Y, Shibata A, Shirasu K, Aoki N, Sugita R, Ogawa T, Suzuki H, Iwata R, Nakanishi TM, Tanoi K. Short-Term Magnesium Deficiency Triggers Nutrient Retranslocation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:563. [PMID: 32582226 PMCID: PMC7287120 DOI: 10.3389/fpls.2020.00563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/15/2020] [Indexed: 05/03/2023]
Abstract
Magnesium (Mg) is essential for many biological processes in plant cells, and its deficiency causes yield reduction in crop systems. Low Mg status reportedly affects photosynthesis, sucrose partitioning and biomass allocation. However, earlier physiological responses to Mg deficiency are scarcely described. Here, we report that Mg deficiency in Arabidopsis thaliana first modified the mineral profile in mature leaves within 1 or 2 days, then affected sucrose partitioning after 4 days, and net photosynthesis and biomass production after 6 days. The short-term Mg deficiency reduced the contents of phosphorus (P), potassium, manganese, zinc and molybdenum in mature but not in expanding (young) leaves. While P content decreased in mature leaves, P transport from roots to mature leaves was not affected, indicating that Mg deficiency triggered retranslocation of the mineral nutrients from mature leaves. A global transcriptome analysis revealed that Mg deficiency triggered the expression of genes involved in defence response in young leaves.
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Affiliation(s)
- Takaaki Ogura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Natsuko I. Kobayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, Brussels, Belgium
| | | | - Arisa Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Naohiro Aoki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryohei Sugita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takahiro Ogawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Suzuki
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Ren Iwata
- Cyclotron and Radioisotope Center, Tohoku University, Sendai, Japan
| | - Tomoko M. Nakanishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Hoshi University, Tokyo, Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
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Dysregulation of Magnesium Transport Protects Bacillus subtilis against Manganese and Cobalt Intoxication. J Bacteriol 2020; 202:JB.00711-19. [PMID: 31964700 DOI: 10.1128/jb.00711-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
Transition metals are essential for life but are toxic when in excess. Metal ion intoxication may result from the mismetallation of essential metal-dependent enzymes with a noncognate metal. To begin to identify enzymes and processes that are susceptible to mismetallation, we have selected for strains with increased resistance to Mn(II) and Co(II). In Bacillus subtilis, cells lacking the MntR metalloregulator are exquisitely sensitive to Mn(II) but can easily become resistant by acquiring mutations affecting the MntH Mn(II) importer. Using transposon mutagenesis, and starting with an mntR mntH strain, we recovered mariner insertions that inactivated the mpfA gene encoding a putative Mg(II) efflux system. Loss of MpfA leads to elevated intracellular Mg(II), increased sensitivity to high Mg(II), and reduced Mn(II) sensitivity. Consistently, we also recovered an insertion disrupting the mgtE riboswitch, which normally restricts expression of the major Mg(II) importer. These results suggest that Mn(II) intoxication results from disruption of a Mg(II)-dependent enzyme or process. Mutations that inactivate MpfA were also recovered in a selection for Co(II) resistance beginning with sensitized strains lacking the major Co(II) efflux pump, CzcD. Since both Mn(II) and Co(II) may mismetallate iron-dependent enzymes, we repeated the selections under conditions of iron depletion imposed by expression of the Listeria monocytogenes FrvA iron exporter. Under conditions of iron depletion, a wider variety of suppressor mutations were recovered, but they still point to a central role for Mg(II) in maintaining metal ion homeostasis.IMPORTANCE Cellular metal ion homeostasis is tightly regulated. When metal ion levels are imbalanced, or when one metal is at toxic levels, enzymes may bind to the wrong metal cofactor. Enzyme mismetallation can impair metabolism, lead to new and deleterious reactions, and cause cell death. Beginning with Bacillus subtilis strains genetically sensitized to metal intoxication through loss of efflux or by lowering intracellular iron, we identified mutations that suppress the deleterious effects of excess Mn(II) or Co(II). For both metals, mutations in mpfA, encoding a Mg(II) efflux pump, suppressed toxicity. These mutant strains have elevated intracellular Mg(II), suggesting that Mg(II)-dependent processes are very sensitive to disruption by transition metals.
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Abstract
Bacterial persisters emerge and increase in numbers over time as a bacterial culture grows from log phase to stationary phase. However, the underlying basis of the inevitable tendency is unclear. In this study, we investigated the role of nutrients in starvation-mediated persister formation of Staphylococcus aureus By screening of nutrient components, we found that starvation-induced persister formation of log-phase cultures could be reversed by addition of magnesium (Mg2+) but not amino acids, nucleotides, or other salts. Further, deprivation of extracellular Mg2+ reduced cytoplasmic ATP, inducing persistence without affecting cytoplasmic Mg2+ or membrane potential. Finally, we showed that Mg2+ reduced expression of stationary cell marker genes, cap5A and arcA These findings indicate a connection between Mg2+ levels and ATP, which represents metabolic status and mediates antibiotic persistence during growth.IMPORTANCE Various genes have been identified to be involved in bacterial persister formation regardless of the presence or absence of persister genes. Despite recent discoveries of the roles of ATP and membrane potential in persister formation, the key element that triggers change of ATP or membrane potential remains elusive. Our work demonstrates that Mg2+ instead of other ions or nutrient components is the key element for persistence by inducing a decrease of cytoplasmic ATP, which subsequently induces persister formation. In addition, we observed tight regulation of genes for Mg2+ transport in different growth phases in S. aureus These findings indicate that despite being a key nutrient, Mg2+ also served as a key signal in persister formation during growth.
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Harris KA, Odzer NB, Breaker RR. Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans. Mol Microbiol 2019; 112:1552-1563. [PMID: 31461569 DOI: 10.1111/mmi.14379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
OLE RNAs represent an unusual class of bacterial noncoding RNAs common in Gram-positive anaerobes. The OLE RNA of the alkaliphile Bacillus halodurans is highly expressed and naturally interacts with at least two RNA-binding proteins called OapA and OapB. The phenotypes of the corresponding knockouts include growth inhibition when exposed to ethanol or other short-chain alcohols or when incubated at modestly reduced temperatures (e.g. 20°C). Intriguingly, the OapA 'PM1' mutant, which carries two amino acid changes to a highly conserved region, yields a dominant-negative phenotype that causes more severe growth defects under these same stress conditions. Herein, we report that the PM1 strain also exhibits extreme sensitivity to elevated Mg2+ concentrations, beginning as low as 2 mM. Suppressor mutants predominantly map to genes for aconitate hydratase and isocitrate dehydrogenase, which are expected to alter cellular citrate concentrations. Citrate reduces the severity of the Mg2+ toxicity phenotype, but neither the genomic mutations nor the addition of citrate to the medium overcomes ethanol toxicity or temperature sensitivity. These findings reveal that OLE RNA and its protein partners are involved in biochemical responses under several stress conditions, wherein the unusual sensitivity to Mg2+ can be independently suppressed by specific genomic mutations.
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Affiliation(s)
- Kimberly A Harris
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Nicole B Odzer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ronald R Breaker
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Magnesium Is a Key Player in Neuronal Maturation and Neuropathology. Int J Mol Sci 2019; 20:ijms20143439. [PMID: 31336935 PMCID: PMC6678825 DOI: 10.3390/ijms20143439] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023] Open
Abstract
Magnesium (Mg) is the second most abundant cation in mammalian cells, and it is essential for numerous cellular processes including enzymatic reactions, ion channel functions, metabolic cycles, cellular signaling, and DNA/RNA stabilities. Because of the versatile and universal nature of Mg2+, the homeostasis of intracellular Mg2+ is physiologically linked to growth, proliferation, differentiation, energy metabolism, and death of cells. On the cellular and tissue levels, maintaining Mg2+ within optimal levels according to the biological context, such as cell types, developmental stages, extracellular environments, and pathophysiological conditions, is crucial for development, normal functions, and diseases. Hence, Mg2+ is pathologically involved in cancers, diabetes, and neurodegenerative diseases, such as Parkinson's disease, Alzheimer's disease, and demyelination. In the research field regarding the roles and mechanisms of Mg2+ regulation, numerous controversies caused by its versatility and complexity still exist. As Mg2+, at least, plays critical roles in neuronal development, healthy normal functions, and diseases, appropriate Mg2+ supplementation exhibits neurotrophic effects in a majority of cases. Hence, the control of Mg2+ homeostasis can be a candidate for therapeutic targets in neuronal diseases. In this review, recent results regarding the roles of intracellular Mg2+ and its regulatory system in determining the cell phenotype, fate, and diseases in the nervous system are summarized, and an overview of the comprehensive roles of Mg2+ is provided.
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Lee DYD, Galera-Laporta L, Bialecka-Fornal M, Moon EC, Shen Z, Briggs SP, Garcia-Ojalvo J, Süel GM. Magnesium Flux Modulates Ribosomes to Increase Bacterial Survival. Cell 2019; 177:352-360.e13. [PMID: 30853217 PMCID: PMC6814349 DOI: 10.1016/j.cell.2019.01.042] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/03/2018] [Accepted: 01/24/2019] [Indexed: 01/30/2023]
Abstract
Bacteria exhibit cell-to-cell variability in their resilience to stress, for example, following antibiotic exposure. Higher resilience is typically ascribed to "dormant" non-growing cellular states. Here, by measuring membrane potential dynamics of Bacillus subtilis cells, we show that actively growing bacteria can cope with ribosome-targeting antibiotics through an alternative mechanism based on ion flux modulation. Specifically, we observed two types of cellular behavior: growth-defective cells exhibited a mathematically predicted transient increase in membrane potential (hyperpolarization), followed by cell death, whereas growing cells lacked hyperpolarization events and showed elevated survival. Using structural perturbations of the ribosome and proteomic analysis, we uncovered that stress resilience arises from magnesium influx, which prevents hyperpolarization. Thus, ion flux modulation provides a distinct mechanism to cope with ribosomal stress. These results suggest new approaches to increase the effectiveness of ribosome-targeting antibiotics and reveal an intriguing connection between ribosomes and the membrane potential, two fundamental properties of cells.
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Affiliation(s)
- Dong-Yeon D Lee
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leticia Galera-Laporta
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Maja Bialecka-Fornal
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eun Chae Moon
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhouxin Shen
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0380, USA
| | - Steven P Briggs
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093-0380, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093-0380, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093-0380, USA.
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32
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Heeney DD, Yarov-Yarovoy V, Marco ML. Sensitivity to the two peptide bacteriocin plantaricin EF is dependent on CorC, a membrane-bound, magnesium/cobalt efflux protein. Microbiologyopen 2019; 8:e827. [PMID: 30891921 PMCID: PMC6854853 DOI: 10.1002/mbo3.827] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 12/12/2022] Open
Abstract
Lactic acid bacteria produce a variety of antimicrobial peptides known as bacteriocins. Most bacteriocins are understood to kill sensitive bacteria through receptor‐mediated disruptions. Here, we report on the identification of the Lactobacillus plantarum plantaricin EF (PlnEF) receptor. Spontaneous PlnEF‐resistant mutants of the PlnEF‐indicator strain L. plantarum NCIMB 700965 (LP965) were isolated and confirmed to maintain cellular ATP levels in the presence of PlnEF. Genome comparisons resulted in the identification of a single mutated gene annotated as the membrane‐bound, magnesium/cobalt efflux protein CorC. All isolates contained a valine (V) at position 334 instead of a glycine (G) in a cysteine‐β‐synthase domain at the C‐terminal region of CorC. In silico template‐based modeling of this domain indicated that the mutation resides in a loop between two β‐strands. The relationship between PlnEF, CorC, and metal homeostasis was supported by the finding that PlnEF‐resistance was lost when PlnEF was applied together with high concentrations of Mg2+, Co2+, Zn2+, or Cu2+. Lastly, PlnEF sensitivity was increased upon heterologous expression of LP965 corC but not the G334V CorC mutant in the PlnEF‐resistant strain Lactobacillus casei BL23. These results show that PlnEF kills sensitive bacteria by targeting CorC.
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Affiliation(s)
- Dustin D Heeney
- Department of Food Science & Technology, University of California-Davis, Davis, California
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California
| | - Maria L Marco
- Department of Food Science & Technology, University of California-Davis, Davis, California
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33
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Uzawa K, Kasamatsu A, Saito T, Kita A, Sawai Y, Toeda Y, Koike K, Nakashima D, Endo Y, Shiiba M, Takiguchi Y, Tanzawa H. Growth suppression of human oral cancer cells by candidate agents for cetuximab-side effects. Exp Cell Res 2019; 376:210-220. [DOI: 10.1016/j.yexcr.2019.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/15/2019] [Accepted: 01/24/2019] [Indexed: 02/02/2023]
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34
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Akanuma G, Tagana T, Sawada M, Suzuki S, Shimada T, Tanaka K, Kawamura F, Kato-Yamada Y. C-terminal regulatory domain of the ε subunit of F o F 1 ATP synthase enhances the ATP-dependent H + pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis. Microbiologyopen 2019; 8:e00815. [PMID: 30809948 PMCID: PMC6692558 DOI: 10.1002/mbo3.815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023] Open
Abstract
The ε subunit of FoF1‐ATPase/synthase (FoF1) plays a crucial role in regulating FoF1 activity. To understand the physiological significance of the ε subunit‐mediated regulation of FoF1 in Bacillus subtilis, we constructed and characterized a mutant harboring a deletion in the C‐terminal regulatory domain of the ε subunit (ε∆C). Analyses using inverted membrane vesicles revealed that the ε∆C mutation decreased ATPase activity and the ATP‐dependent H+‐pumping activity of FoF1. To enhance the effects of ε∆C mutation, this mutation was introduced into a ∆rrn8 strain harboring only two of the 10 rrn (rRNA) operons (∆rrn8 ε∆C mutant strain). Interestingly, growth of the ∆rrn8 ε∆C mutant stalled at late‐exponential phase. During the stalled growth phase, the membrane potential of the ∆rrn8 ε∆C mutant cells was significantly reduced, which led to a decrease in the cellular level of 70S ribosomes. The growth stalling was suppressed by adding glucose into the culture medium. Our findings suggest that the C‐terminal region of the ε subunit is important for alleviating the temporal reduction in the membrane potential, by enhancing the ATP‐dependent H+‐pumping activity of FoF1.
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Affiliation(s)
- Genki Akanuma
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Tomoaki Tagana
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Maho Sawada
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Shota Suzuki
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Tomohiro Shimada
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Yokohama, Midori-ku, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Yokohama, Midori-ku, Japan
| | - Fujio Kawamura
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Yasuyuki Kato-Yamada
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
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Dopp BJL, Tamiev DD, Reuel NF. Cell-free supplement mixtures: Elucidating the history and biochemical utility of additives used to support in vitro protein synthesis in E. coli extract. Biotechnol Adv 2019; 37:246-258. [DOI: 10.1016/j.biotechadv.2018.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/06/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022]
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36
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Kimura T, Lorenz-Fonfria VA, Douki S, Motoki H, Ishitani R, Nureki O, Higashi M, Furutani Y. Vibrational and Molecular Properties of Mg2+ Binding and Ion Selectivity in the Magnesium Channel MgtE. J Phys Chem B 2018; 122:9681-9696. [DOI: 10.1021/acs.jpcb.8b07967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tetsunari Kimura
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Victor A. Lorenz-Fonfria
- Institute of Molecular Science (ICMol), Universitat de València, Catedràtic José Beltrán Martínez 2, 46980 Paterna, Spain
- Department of Biochemistry and Molecular Biology, Universitat de València, Carrer Doctor Moliner 50, 46100 Burjassot, Spain
| | - Shintaro Douki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideyoshi Motoki
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Nakagami, Okinawa 903-0213, Japan
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Nakagami, Okinawa 903-0213, Japan
| | - Yuji Furutani
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
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Magnesium Suppresses Defects in the Formation of 70S Ribosomes as Well as in Sporulation Caused by Lack of Several Individual Ribosomal Proteins. J Bacteriol 2018; 200:JB.00212-18. [PMID: 29967120 DOI: 10.1128/jb.00212-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/25/2018] [Indexed: 01/03/2023] Open
Abstract
Individually, the ribosomal proteins L1, L23, L36, and S6 are not essential for cell proliferation of Bacillus subtilis, but the absence of any one of these ribosomal proteins causes a defect in the formation of the 70S ribosomes and a reduced growth rate. In mutant strains individually lacking these ribosomal proteins, the cellular Mg2+ content was significantly reduced. The deletion of YhdP, an exporter of Mg2+, and overexpression of MgtE, the main importer of Mg2+, increased the cellular Mg2+ content and restored the formation of 70S ribosomes in these mutants. The increase in the cellular Mg2+ content improved the growth rate and the cellular translational activity of the ΔrplA (L1) and the ΔrplW (L23) mutants but did not restore those of the ΔrpmJ (L36) and the ΔrpsF (S6) mutants. The lack of L1 caused a decrease in the production of Spo0A, the master regulator of sporulation, resulting in a decreased sporulation frequency. However, deletion of yhdP and overexpression of mgtE increased the production of Spo0A and partially restored the sporulation frequency in the ΔrplA (L1) mutant. These results indicate that Mg2+ can partly complement the function of several ribosomal proteins, probably by stabilizing the conformation of the ribosome.IMPORTANCE We previously reported that an increase in cellular Mg2+ content can suppress defects in 70S ribosome formation and growth rate caused by the absence of ribosomal protein L34. In the present study, we demonstrated that, even in mutants lacking individual ribosomal proteins other than L34 (L1, L23, L36, and S6), an increase in the cellular Mg2+ content could restore 70S ribosome formation. Moreover, the defect in sporulation caused by the absence of L1 was also suppressed by an increase in the cellular Mg2+ content. These findings indicate that at least part of the function of these ribosomal proteins can be complemented by Mg2+, which is essential for all living cells.
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38
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Guedes-Monteiro RF, Ferreira-Junior JR, Bleicher L, Nóbrega FG, Barrientos A, Barros MH. Mitochondrial ribosome bL34 mutants present diminished translation of cytochrome c oxidase subunits. Cell Biol Int 2017; 42:630-642. [PMID: 29160602 DOI: 10.1002/cbin.10913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/19/2017] [Indexed: 12/31/2022]
Abstract
Saccharomyces cerevisiae mitoribosomes are specialized in the translation of a few number of highly hydrophobic membrane proteins, components of the oxidative phosphorylation system. Mitochondrial characteristics, such as the membrane system and its redox state driven mitoribosomes evolution through great diversion from their bacterial and cytosolic counterparts. Therefore, mitoribosome presents a considerable number of mitochondrial-specific proteins, as well as new protein extensions. In this work we characterize temperature sensitive mutants of the subunit bL34 present in the 54S large subunit. Although bL34 has bacterial homologs, in yeast it has a long 65 aminoacids mitochondrial N-terminal addressing sequence, here we demonstrate that it can be replaced by the mitochondrial addressing sequence of Neurospora crassa ATP9 gene. The bL34 temperature sensitive mutants present lowered translation of mitochondrial COX1 and COX3, which resulted in reduced cytochrome c oxidase activity and respiratory growth deficiency. The sedimentation properties of bL34 in sucrose gradients suggest that similarly to its bacterial homolog, bL34 is also a later participant in the process of mitoribosome biogenesis.
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Affiliation(s)
| | | | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia - Instituto de Ciências Biológicas - Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Mario H Barros
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
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Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C. Extremophiles 2017; 21:963-979. [PMID: 28894932 PMCID: PMC5674127 DOI: 10.1007/s00792-017-0956-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/11/2017] [Indexed: 11/29/2022]
Abstract
Temperature is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ~30 °C, but the deep subsurface bacterium Kosmotoga olearia can grow over a temperature range of 59 °C (20–79 °C). To identify genes correlated with this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65 °C to those at 30, 40, and 77 °C. The temperature treatments affected expression of 573 of 2224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures. At sub-optimal temperatures, many transcriptional changes were similar to those observed in mesophilic bacteria at physiologically low temperatures, including up-regulation of typical cold stress genes and ribosomal proteins. Comparative genomic analysis of additional Thermotogae genomes indicates that one of K. olearia’s strategies for low-temperature growth is increased copy number of some typical cold response genes through duplication and/or lateral acquisition. At 77 °C one-third of the up-regulated genes are of hypothetical function, indicating that many features of high-temperature growth are unknown.
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40
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Gholami Tilko P, Hajihassan Z, Moghimi H. Optimization of recombinant β-NGF expression in Escherichia coli using response surface methodology. Prep Biochem Biotechnol 2017; 47:406-413. [PMID: 27813712 DOI: 10.1080/10826068.2016.1252927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Human nerve growth factor a member of the neurotrophin family can be used to treat neurodegenerative diseases. As it has disulfide bonds in its structure, periplasmic expression of it using appropriate signal sequence is beneficial. Therefore, in this work β-nerve growth factor (β-NGF) was expressed in Escherichia coli using pET39b expression vector containing DsbA signal sequence. In an initial step, the effect of isopropyl β-D-1-thiogalactopyranoside (IPTG) and lactose concentration as inducer on protein production was investigated using response surface methodology. Then the effect of different postinduction time and temperature on protein production was studied. Our results indicated that the highest β-NGF production was achieved with 1 mM IPTG and low concentrations of lactose (0-2% w/v), low cultivation temperature of 25°C and postinduction time of 2 hr. Also following β-NGF purification, bioassay test using PC12 cell line was done. The biological activity of the purified β-NGF showed a similar cell proliferation activity with the standard recombinant human β-NGF. In conclusion, the results indicated an optimized upstream process to obtain high yields of biologically active β-NGF.
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Affiliation(s)
- Pouria Gholami Tilko
- a Department of Life Science Engineering, Faculty of New Sciences and Technologies , University of Tehran , Tehran , Iran.,b Department of Microbial Biotechnology, School of Biology, College of Science , University of Tehran , Tehran , Iran
| | - Zahra Hajihassan
- a Department of Life Science Engineering, Faculty of New Sciences and Technologies , University of Tehran , Tehran , Iran
| | - Hamid Moghimi
- b Department of Microbial Biotechnology, School of Biology, College of Science , University of Tehran , Tehran , Iran
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Pontes MH, Yeom J, Groisman EA. Reducing Ribosome Biosynthesis Promotes Translation during Low Mg 2+ Stress. Mol Cell 2016; 64:480-492. [PMID: 27746019 DOI: 10.1016/j.molcel.2016.05.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/31/2016] [Accepted: 05/05/2016] [Indexed: 12/30/2022]
Abstract
The synthesis of ribosomes is regulated by both amino acid abundance and the availability of ATP, which regenerates guanosine triphosphate (GTP), powers ribosomes, and promotes transcription of rRNA genes. We now report that bacteria supersede both of these controls when experiencing low cytosolic magnesium (Mg2+), a divalent cation essential for ribosome stabilization and for neutralization of ATP's negative charge. We uncover a regulatory circuit that responds to low cytosolic Mg2+ by promoting expression of proteins that import Mg2+ and lower ATP amounts. This response reduces the levels of ATP and ribosomes, making Mg2+ ions available for translation. Mutants defective in Mg2+ uptake and unable to reduce ATP levels accumulate non-functional ribosomal components and undergo translational arrest. Our findings establish a paradigm whereby cells reduce the amounts of translating ribosomes to carry out protein synthesis.
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Affiliation(s)
- Mauricio H Pontes
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA; Yale Microbial Sciences Institute, PO Box 27389, West Haven, CT 06516, USA
| | - Jinki Yeom
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA; Yale Microbial Sciences Institute, PO Box 27389, West Haven, CT 06516, USA.
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A novel type bacterial flagellar motor that can use divalent cations as a coupling ion. Sci Rep 2016; 6:19773. [PMID: 26794857 PMCID: PMC4726428 DOI: 10.1038/srep19773] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 12/18/2015] [Indexed: 12/25/2022] Open
Abstract
The bacterial flagellar motor is a sophisticated nanomachine embedded in the cell envelope and powered by an electrochemical gradient of H(+), Na(+), or K(+)across the cytoplasmic membrane. Here we describe a new member of the bacterial flagellar stator channel family (MotAB1 of Paenibacillus sp. TCA20 (TCA-MotAB1)) that is coupled to divalent cations (Ca(2+)and Mg(2+)). In the absence of divalent cations of alkaline earth metals, no swimming was observed in Paenibacillus sp. TCA20, which grows optimally in Ca(2+)-rich environments. This pattern was confirmed by swimming assays of a stator-free Bacillus subtilis mutant expressing TCA-MotAB1. Both a stator-free and major Mg(2+)uptake system-deleted B. subtilis mutant expressing TCA-MotAB1 complemented both growth and motility deficiency under low Mg(2+)conditions and exhibited [Mg(2+)]in identical to that of the wild-type. This is the first report of a flagellar motor that can use Ca(2+)and Mg(2+)as coupling ions. These findings will promote the understanding of the operating principles of flagellar motors and molecular mechanisms of ion selectivity.
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Liu H, Liang S, Yang X, Ji Z, Zhao W, Ye X, Rui J. RNAi-mediated RPL34 knockdown suppresses the growth of human gastric cancer cells. Oncol Rep 2015; 34:2267-72. [PMID: 26323242 PMCID: PMC4583519 DOI: 10.3892/or.2015.4219] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/07/2015] [Indexed: 01/23/2023] Open
Abstract
An increasing body of evidence suggests that ribosomal proteins may have ribosome-independent functions and may be involved in various physiological and pathological processes. To examine the role of ribosomal protein L34 (RPL34) in cancer transformation, we assessed its expression in gastric cancer cell lines and found it highly expressed. We further used lentivirus-mediated small interfering RNAs (siRNAs) to knockdown RPL34 expression in the human gastric cancer cell line SGC-7901. RNA interference (RNAi)-mediated inhibition of RPL34 expression in SGC-7901 cells significantly suppressed cell proliferation, increased apoptosis and arrested cells in the S phase. The results of the present study suggest that RPL34 plays a critical role in cell proliferation, cell cycle distribution and apoptosis of human malignant gastric cells.
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Affiliation(s)
- Hui Liu
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Shaohua Liang
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Xi Yang
- Department of Oncology, Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Zhaoning Ji
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Wenying Zhao
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Xiaobing Ye
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
| | - Jing Rui
- Department of Medical Oncology, Yijishan Hospital of Wannan Medical College, Wuhu, Anhui 241001, P.R. China
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When Too Much ATP Is Bad for Protein Synthesis. J Mol Biol 2015; 427:2586-2594. [PMID: 26150063 DOI: 10.1016/j.jmb.2015.06.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 01/17/2023]
Abstract
Adenosine triphosphate (ATP) is the energy currency of living cells. Even though ATP powers virtually all energy-dependent activities, most cellular ATP is utilized in protein synthesis via tRNA aminoacylation and guanosine triphosphate regeneration. Magnesium (Mg(2+)), the most common divalent cation in living cells, plays crucial roles in protein synthesis by maintaining the structure of ribosomes, participating in the biochemistry of translation initiation and functioning as a counterion for ATP. A non-physiological increase in ATP levels hinders growth in cells experiencing Mg(2+) limitation because ATP is the most abundant nucleotide triphosphate in the cell, and Mg(2+) is also required for the stabilization of the cytoplasmic membrane and as a cofactor for essential enzymes. We propose that organisms cope with Mg(2+) limitation by decreasing ATP levels and ribosome production, thereby reallocating Mg(2+) to indispensable cellular processes.
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Zielke RA, Wierzbicki IH, Baarda BI, Sikora AE. The Neisseria gonorrhoeae Obg protein is an essential ribosome-associated GTPase and a potential drug target. BMC Microbiol 2015; 15:129. [PMID: 26122105 PMCID: PMC4487204 DOI: 10.1186/s12866-015-0453-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background Neisseria gonorrhoeae (GC) is a Gram-negative pathogen that most commonly infects mucosal surfaces, causing sexually transmitted urethritis in men and endocervicitis in women. Serious complications associated with these infections are frequent and include pelvic inflammatory disease, ectopic pregnancy, and infertility. The incidence of gonorrhea cases remains high globally while antibiotic treatment options, the sole counter measures against gonorrhea, are declining due to the remarkable ability of GC to acquire resistance. Evaluating of potential drug targets is essential to provide opportunities for developing antimicrobials with new mechanisms of action. We propose the GC Obg protein, belonging to the Obg/CgtA GTPase subfamily, as a potential target for the development of therapeutic interventions against gonorrhea, and in this study perform its initial functional and biochemical characterization. Results We report that NGO1990 encodes Obg protein, which is an essential factor for GC viability, associates predominantly with the large 50S ribosomal subunit, and is stably expressed under conditions relevant to infection of the human host. The anti-Obg antisera cross-reacts with a panel of contemporary GC clinical isolates, demonstrating the ubiquitous nature of Obg. The cellular levels of Obg reach a maximum in the early logarithmic phase and remain constant throughout bacterial growth. The in vitro binding and hydrolysis of the fluorescent guanine nucleotide analogs mant-GTP and mant-GDP by recombinant wild type and T192AT193A mutated variants of Obg are also assessed. Conclusions Characterization of the GC Obg at the molecular and functional levels presented herein may facilitate the future targeting of this protein with small molecule inhibitors and the evaluation of identified lead compounds for bactericidal activity against GC and other drug-resistant bacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0453-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Igor H Wierzbicki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Benjamin I Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
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Abstract
RNase E is a major intracellular endoribonuclease in many bacteria and participates in most aspects of RNA processing and degradation. RNase E requires a divalent metal ion for its activity. We show that only Mg(2+) and Mn(2+) will support significant rates of activity in vitro against natural RNAs, with Mn(2+) being preferred. Both Mg(2+) and Mn(2+) also support cleavage of an oligonucleotide substrate with similar kinetic parameters for both ions. Salts of Ni(2+) and Zn(2+) permitted low levels of activity, while Ca(2+), Co(3+), Cu(2+), and Fe(2+) did not. A mutation to one of the residues known to chelate Mg(2+), D346C, led to almost complete loss of activity dependent on Mg(2+); however, the activity of the mutant enzyme was fully restored by the presence of Mn(2+) with kinetic parameters fully equivalent to those of wild-type enzyme. A similar mutation to the other chelating residue, D303C, resulted in nearly full loss of activity regardless of metal ion. The properties of RNase E D346C enabled a test of the ionic requirements of RNase E in vivo. Plasmid shuffling experiments showed that both rneD303C (i.e., the rne gene encoding a D-to-C change at position 303) and rneD346C were inviable whether or not the selection medium was supplied with MnSO4, implying that RNase E relies on Mg(2+) exclusively in vivo.
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Abstract
Mg(2+) and K(+) are the prevalent di- and monovalent cations inside the cells in all three domains, playing a dominant role in structure and function of biological macromolecules. Ribosomes bind a substantial fraction of total Mg(2+) and K(+) cations. In this issue of the Journal of Bacteriology, Akanuma and coworkers (G. Akanuma et al., J. Bacteriol. 196:3820-3830, 2014, doi:10.1128/JB.01896-14) report a surprising genetic link between ribosome amounts per cell and the intracellular Mg(2+) concentrations.
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