1
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Fernando CM, Breaker RR. Bioinformatic prediction of proteins relevant to functions of the bacterial OLE ribonucleoprotein complex. mSphere 2024; 9:e0015924. [PMID: 38771028 DOI: 10.1128/msphere.00159-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
OLE (ornate, large, extremophilic) RNAs are members of a noncoding RNA class present in many Gram-positive, extremophilic bacteria. The large size, complex structure, and extensive sequence conservation of OLE RNAs are characteristics consistent with the hypothesis that they likely function as ribozymes. The OLE RNA representative from Halalkalibacterium halodurans is known to localize to the phospholipid membrane and requires at least three essential protein partners: OapA, OapB, and OapC. However, the precise biochemical functions of this unusual ribonucleoprotein (RNP) complex remain unknown. Genetic disruption of OLE RNA or its partners revealed that the complex is beneficial under diverse stress conditions. To search for additional links between OLE RNA and other cellular components, we used phylogenetic profiling to identify proteins that are either correlated or anticorrelated with the presence of OLE RNA in various bacterial species. This analysis revealed strong correlations between the essential protein-binding partners of OLE RNA and organisms that carry the ole gene. Similarly, proteins involved in sporulation are correlated, suggesting a potential role for the OLE RNP complex in spore formation. Intriguingly, the Mg2+ transporter MpfA is strongly anticorrelated with OLE RNA. Evidence indicates that MpfA is structurally related to OapA and therefore MpfA may serve as a functional replacement for some contributions otherwise performed by the OLE RNP complex in species that lack this device. Indeed, OLE RNAs might represent an ancient RNA class that enabled primitive organisms to sense and respond to major cellular stresses.IMPORTANCEOLE (ornate, large, extremophilic) RNAs were first reported nearly 20 years ago, and they represent one of the largest and most intricately folded noncoding RNA classes whose biochemical function remains to be established. Other RNAs with similar size, structural complexity, and extent of sequence conservation have proven to catalyze chemical transformations. Therefore, we speculate that OLE RNAs likewise operate as ribozymes and that they might catalyze a fundamental reaction that has persisted since the RNA World era-a time before the emergence of proteins in evolution. To seek additional clues regarding the function of OLE RNA, we undertook a computational effort to identify potential protein components of the OLE ribonucleoprotein (RNP) complex or other proteins that have functional links to this device. This analysis revealed known protein partners and several additional proteins that might be physically or functionally linked to the OLE RNP complex. Finally, we identified a Mg2+ transporter protein, MpfA, that strongly anticorrelates with the OLE RNP complex. This latter result suggests that MpfA might perform at least some functions that are like those carried out by the OLE RNP complex.
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Affiliation(s)
- Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
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2
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Bang J, Park J, Lee SH, Jang J, Hwang J, Kamarov O, Park HJ, Lee SJ, Seo MD, Won HS, Seok SH, Kim JH. Nontraditional Roles of Magnesium Ions in Modulating Sav2152: Insight from a Haloacid Dehalogenase-like Superfamily Phosphatase from Staphylococcus aureus. Int J Mol Sci 2024; 25:5021. [PMID: 38732240 PMCID: PMC11084212 DOI: 10.3390/ijms25095021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infection has rapidly spread through various routes. A genomic analysis of clinical MRSA samples revealed an unknown protein, Sav2152, predicted to be a haloacid dehalogenase (HAD)-like hydrolase, making it a potential candidate for a novel drug target. In this study, we determined the crystal structure of Sav2152, which consists of a C2-type cap domain and a core domain. The core domain contains four motifs involved in phosphatase activity that depend on the presence of Mg2+ ions. Specifically, residues D10, D12, and D233, which closely correspond to key residues in structurally homolog proteins, are responsible for binding to the metal ion and are known to play critical roles in phosphatase activity. Our findings indicate that the Mg2+ ion known to stabilize local regions surrounding it, however, paradoxically, destabilizes the local region. Through mutant screening, we identified D10 and D12 as crucial residues for metal binding and maintaining structural stability via various uncharacterized intra-protein interactions, respectively. Substituting D10 with Ala effectively prevents the interaction with Mg2+ ions. The mutation of D12 disrupts important structural associations mediated by D12, leading to a decrease in the stability of Sav2152 and an enhancement in binding affinity to Mg2+ ions. Additionally, our study revealed that D237 can replace D12 and retain phosphatase activity. In summary, our work uncovers the novel role of metal ions in HAD-like phosphatase activity.
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Affiliation(s)
- Jaeseok Bang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Jaehui Park
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Sung-Hee Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Jinhwa Jang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Junwoo Hwang
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Otabek Kamarov
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Hae-Joon Park
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Soo-Jae Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea;
- College of Pharmacy, Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon 16499, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea;
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Republic of Korea
| | - Seung-Hyeon Seok
- College of Pharmacy, Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 632433, Republic of Korea
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Republic of Korea; (J.B.); (J.P.); (S.-H.L.); (J.J.); (J.H.); (O.K.); (H.-J.P.); (S.-J.L.)
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3
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Sarıgül İ, Žukova A, Alparslan E, Remm S, Pihlak M, Kaldalu N, Tenson T, Maiväli Ü. Involvement of Escherichia coli YbeX/CorC in ribosomal metabolism. Mol Microbiol 2024; 121:984-1001. [PMID: 38494741 DOI: 10.1111/mmi.15248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/19/2024]
Abstract
YbeX of Escherichia coli, a member of the CorC protein family, is encoded in the same operon with ribosome-associated proteins YbeY and YbeZ. Here, we report the involvement of YbeX in ribosomal metabolism. The ΔybeX cells accumulate distinct 16S rRNA degradation intermediates in the 30S particles and the 70S ribosomes. E. coli lacking ybeX has a lengthened lag phase upon outgrowth from the stationary phase. This growth phenotype is heterogeneous at the individual cell level and especially prominent under low extracellular magnesium levels. The ΔybeX strain is sensitive to elevated growth temperatures and to several ribosome-targeting antibiotics that have in common the ability to induce the cold shock response in E. coli. Although generally milder, the phenotypes of the ΔybeX mutant overlap with those caused by ybeY deletion. A genetic screen revealed partial compensation of the ΔybeX growth phenotype by the overexpression of YbeY. These findings indicate an interconnectedness among the ybeZYX operon genes, highlighting their roles in ribosomal assembly and/or degradation.
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Affiliation(s)
- İsmail Sarıgül
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Amata Žukova
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Emel Alparslan
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sille Remm
- Institute of Technology, University of Tartu, Tartu, Estonia
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Margus Pihlak
- Department of Cybernetics, Tallinn University of Technology, Tallinn, Estonia
| | - Niilo Kaldalu
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ülo Maiväli
- Institute of Technology, University of Tartu, Tartu, Estonia
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4
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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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5
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Elston R, Mulligan C, Thomas GH. Flipping the switch: dynamic modulation of membrane transporter activity in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37948297 DOI: 10.1099/mic.0.001412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The controlled entry and expulsion of small molecules across the bacterial cytoplasmic membrane is essential for efficient cell growth and cellular homeostasis. While much is known about the transcriptional regulation of genes encoding transporters, less is understood about how transporter activity is modulated once the protein is functional in the membrane, a potentially more rapid and dynamic level of control. In this review, we bring together literature from the bacterial transport community exemplifying the extensive and diverse mechanisms that have evolved to rapidly modulate transporter function, predominantly by switching activity off. This includes small molecule feedback, inhibition by interaction with small peptides, regulation through binding larger signal transduction proteins and, finally, the emerging area of controlled proteolysis. Many of these examples have been discovered in the context of metal transport, which has to finely balance active accumulation of elements that are essential for growth but can also quickly become toxic if intracellular homeostasis is not tightly controlled. Consistent with this, these transporters appear to be regulated at multiple levels. Finally, we find common regulatory themes, most often through the fusion of additional regulatory domains to transporters, which suggest the potential for even more widespread regulation of transporter activity in biology.
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Affiliation(s)
- Rory Elston
- Department of Biology, University of York, York, UK
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6
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Breaker RR, Harris KA, Lyon SE, Wencker FDR, Fernando CM. Evidence that OLE RNA is a component of a major stress-responsive ribonucleoprotein particle in extremophilic bacteria. Mol Microbiol 2023; 120:324-340. [PMID: 37469248 DOI: 10.1111/mmi.15129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/30/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
OLE RNA is a ~600-nucleotide noncoding RNA present in many Gram-positive bacteria that thrive mostly in extreme environments, including elevated temperature, salt, and pH conditions. The precise biochemical functions of this highly conserved RNA remain unknown, but it forms a ribonucleoprotein (RNP) complex that localizes to cell membranes. Genetic disruption of the RNA or its essential protein partners causes reduced cell growth under various stress conditions. These phenotypes include sensitivity to short-chain alcohols, cold intolerance, reduced growth on sub-optimal carbon sources, and intolerance of even modest concentrations of Mg2+ . Thus, many bacterial species appear to employ OLE RNA as a component of an intricate RNP apparatus to monitor fundamental cellular processes and make physiological and metabolic adaptations. Herein we hypothesize that the OLE RNP complex is functionally equivalent to the eukaryotic TOR complexes, which integrate signals from various diverse pathways to coordinate processes central to cell growth, replication, and survival.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Kimberly A Harris
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Seth E Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Freya D R Wencker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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7
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Lyon SE, Harris KA, Odzer NB, Wilkins SG, Breaker RR. Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function. J Biol Chem 2022; 298:102674. [PMID: 36336078 PMCID: PMC9723947 DOI: 10.1016/j.jbc.2022.102674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022] Open
Abstract
Ornate, large, extremophilic (OLE) RNAs represent a class of noncoding RNAs prevalent in Gram-positive, extremophilic/anaerobic bacterial species. OLE RNAs (∼600 nt), whose precise biochemical functions remain mysterious, form an intricate secondary structure interspersed with regions of highly conserved nucleotides. In the alkali-halophilic bacterium Bacillus halodurans, OLE RNA is a component of a ribonucleoprotein (RNP) complex involving at least two proteins named OapA and OapB, but additional components may exist that could point to functional roles for the RNA. Disruption of the genes for either OLE RNA, OapA, or OapB result in the inability of cells to overcome cold, alcohol, or Mg2+ stresses. In the current study, we used in vivo crosslinking followed by OLE RNA isolation to identify the protein YbxF as a potential additional partner in the OLE RNP complex. Notably, a mutation in the gene for this same protein was also reported to be present in a strain wherein the complex is nonfunctional. The B. halodurans YbxF (herein renamed OapC) is homologous to a bacterial protein earlier demonstrated to bind kink turn (k-turn) RNA structural motifs. In vitro RNA-protein binding assays reveal that OLE RNA forms a previously unrecognized k-turn that serves as the natural binding site for YbxF/OapC. Moreover, B. halodurans cells carrying OLE RNAs with disruptive mutations in the k-turn exhibit phenotypes identical to cells lacking functional OLE RNP complexes. These findings reveal that the YbxF/OapC protein of B. halodurans is important for the formation of a functional OLE RNP complex.
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Affiliation(s)
- Seth E Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Kimberly A Harris
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nicole B Odzer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Sarah G Wilkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA; Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA.
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8
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Inoue S, Hayashi M, Huang S, Yokosho K, Gotoh E, Ikematsu S, Okumura M, Suzuki T, Kamura T, Kinoshita T, Ma JF. A tonoplast-localized magnesium transporter is crucial for stomatal opening in Arabidopsis under high Mg 2+ conditions. THE NEW PHYTOLOGIST 2022; 236:864-877. [PMID: 35976788 PMCID: PMC9804957 DOI: 10.1111/nph.18410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Plant stomata play an important role in CO2 uptake for photosynthesis and transpiration, but the mechanisms underlying stomatal opening and closing under changing environmental conditions are still not completely understood. Through large-scale genetic screening, we isolated an Arabidopsis mutant (closed stomata2 (cst2)) that is defective in stomatal opening. We cloned the causal gene (MGR1/CST2) and functionally characterized this gene. The mutant phenotype was caused by a mutation in a gene encoding an unknown protein with similarities to the human magnesium (Mg2+ ) efflux transporter ACDP/CNNM. MGR1/CST2 was localized to the tonoplast and showed transport activity for Mg2+ . This protein was constitutively and highly expressed in guard cells. Knockout of this gene resulted in stomatal closing, decreased photosynthesis and growth retardation, especially under high Mg2+ conditions, while overexpression of this gene increased stomatal opening and tolerance to high Mg2+ concentrations. Furthermore, guard cell-specific expression of MGR1/CST2 in the mutant partially restored its stomatal opening. Our results indicate that MGR1/CST2 expression in the leaf guard cells plays an important role in maintaining cytosolic Mg2+ concentrations through sequestering Mg2+ into vacuoles, which is required for stomatal opening, especially under high Mg2+ conditions.
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Affiliation(s)
- Shin‐ichiro Inoue
- Division of Biological Science, Graduate School of ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoyaAichi464‐8602Japan
| | - Maki Hayashi
- Division of Biological Science, Graduate School of ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoyaAichi464‐8602Japan
| | - Sheng Huang
- Institute of Plant Science and ResourcesOkayama UniversityChuo 2‐20‐1Kurashiki710‐0046Japan
| | - Kengo Yokosho
- Institute of Plant Science and ResourcesOkayama UniversityChuo 2‐20‐1Kurashiki710‐0046Japan
| | - Eiji Gotoh
- Department of Forest Environmental Sciences, Faculty of AgricultureKyushu University744 MotookaFukuoka819‐0395Japan
| | - Shuka Ikematsu
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityFuro‐cho, ChikusaNagoya464‐8602Japan
| | - Masaki Okumura
- Division of Biological Science, Graduate School of ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoyaAichi464‐8602Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and BiotechnologyChubu UniversityKasugai‐shiAichi487‐8501Japan
| | - Takumi Kamura
- Division of Biological Science, Graduate School of ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoyaAichi464‐8602Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of ScienceNagoya UniversityFuro‐cho, Chikusa‐kuNagoyaAichi464‐8602Japan
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityFuro‐cho, ChikusaNagoya464‐8602Japan
| | - Jian Feng Ma
- Institute of Plant Science and ResourcesOkayama UniversityChuo 2‐20‐1Kurashiki710‐0046Japan
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Zhang B, Zhang C, Tang R, Zheng X, Zhao F, Fu A, Lan W, Luan S. Two magnesium transporters in the chloroplast inner envelope essential for thylakoid biogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:464-478. [PMID: 35776059 DOI: 10.1111/nph.18349] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Magnesium (Mg2+ ) serves as a cofactor for a number of photosynthetic enzymes in the chloroplast, and is the central atom of the Chl molecule. However, little is known about the molecular mechanism of Mg2+ transport across the chloroplast envelope. Here, we report the functional characterization of two transport proteins in Arabidopsis: Magnesium Release 8 (MGR8) and MGR9, of the ACDP/CNNM family, which is evolutionarily conserved across all lineages of living organisms. Both MGR8 and MGR9 genes were expressed ubiquitously, and their encoded proteins were localized in the inner envelope of chloroplasts. Mutations of MGR8 and MGR9 together, but neither of them alone, resulted in albino ovules and chlorotic seedlings. Further analysis revealed severe defects in thylakoid biogenesis and assembly of photosynthetic complexes in the double mutant. Both MGR8 and MGR9 functionally complemented the growth of the Salmonella typhimurium mutant strain MM281, which lacks Mg2+ uptake capacity. The embryonic and early seedling defects of the mgr8/mgr9 double mutant were rescued by the expression of MGR9 under the embryo-specific ABI3 promoter. The partially rescued mutant plants were hypersensitive to Mg2+ deficient conditions and contained less Mg2+ in their chloroplasts than wild-type plants. Taken together, we conclude that MGR8 and MGR9 serve as Mg2+ transporters and are responsible for chloroplast Mg2+ uptake.
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Affiliation(s)
- Bin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Sciences, Northwest University, Xi'an, 710069, China
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Chi Zhang
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Renjie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Xiaojiang Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, China
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Fugeng Zhao
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Aigen Fu
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Wenzhi Lan
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, College of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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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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11
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Meng SF, Zhang B, Tang RJ, Zheng XJ, Chen R, Liu CG, Jing YP, Ge HM, Zhang C, Chu YL, Fu AG, Zhao FG, Luan S, Lan WZ. Four plasma membrane-localized MGR transporters mediate xylem Mg 2+ loading for root-to-shoot Mg 2+ translocation in Arabidopsis. MOLECULAR PLANT 2022; 15:805-819. [PMID: 35063662 DOI: 10.1016/j.molp.2022.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 11/14/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Magnesium (Mg2+), an essential structural component of chlorophyll, is absorbed from the soil by roots and transported to shoots to support photosynthesis in plants. However, the molecular mechanisms underlying root-to-shoot Mg2+ translocation remain largely unknown. We describe here the identification of four plasma membrane (PM)-localized transporters, named Mg2+ release transporters (MGRs), that are critical for root-to-shoot Mg transport in Arabidopsis. Functional complementation assays in a Mg2+-uptake-deficient bacterial strain confirmed that these MGRs conduct Mg2+ transport. PM-localized MGRs (MGR4, MGR5, MGR6, and MGR7) were expressed primarily in root stellar cells and participated in the xylem loading step of the long-distance Mg2+ transport process. In particular, MGR4 and MGR6 played a major role in shoot Mg homeostasis, as their loss-of-function mutants were hypersensitive to low Mg2+ but tolerant to high Mg2+ conditions. Reciprocal grafting analysis further demonstrated that MGR4 functions in the root to determine shoot Mg2+ accumulation and physiological phenotypes caused by both low- and high-Mg2+ stress. Taken together, our study has identified the long-sought transporters responsible for root-to-shoot Mg2+ translocation in plants.
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Affiliation(s)
- Su-Fang Meng
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Bin Zhang
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China; Institute of Future Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China; The Key Laboratory of Western Resources Biology and Biological Technology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ren-Jie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Xiao-Jiang Zheng
- The Key Laboratory of Western Resources Biology and Biological Technology, College of Life Sciences, Northwest University, Xi'an 710069, China; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Rui Chen
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Cong-Ge Liu
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Yan-Ping Jing
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China; The Key Laboratory of Western Resources Biology and Biological Technology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Hai-Man Ge
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Chi Zhang
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China; The Key Laboratory of Western Resources Biology and Biological Technology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan-Li Chu
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Ai-Gen Fu
- The Key Laboratory of Western Resources Biology and Biological Technology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Fu-Geng Zhao
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
| | - Wen-Zhi Lan
- State Key Laboratory for Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China.
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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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Tang RJ, Meng SF, Zheng XJ, Zhang B, Yang Y, Wang C, Fu AG, Zhao FG, Lan WZ, Luan S. Conserved mechanism for vacuolar magnesium sequestration in yeast and plant cells. NATURE PLANTS 2022; 8:181-190. [PMID: 35087208 DOI: 10.1038/s41477-021-01087-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Magnesium (Mg2+) is an essential nutrient for all life forms. In fungal and plant cells, the majority of Mg2+ is stored in the vacuole but mechanisms for Mg2+ transport into the vacuolar store are not fully understood. Here we demonstrate that members of ancient conserved domain proteins (ACDPs) from Saccharomyces cerevisiae and Arabidopsis thaliana function in vacuolar Mg2+ sequestration that enables plant and yeast cells to cope with high levels of external Mg2+. We show that the yeast genome (as well as other fungal genomes) harbour a single ACDP homologue, referred to as MAM3, that functions specifically in vacuolar Mg2+ accumulation and is essential for tolerance to high Mg. In parallel, vacuolar ACDP homologues were identified from Arabidopsis and shown to complement the yeast mutant mam3Δ. An Arabidopsis mutant lacking one of the vacuolar ACDP homologues displayed hypersensitivity to high-Mg conditions and accumulated less Mg in the vacuole compared with the wild type. Taken together, our results suggest that conserved transporters mediate vacuolar Mg2+ sequestration in fungal and plant cells to maintain cellular Mg2+ homeostasis in response to fluctuating Mg2+ levels in the environment.
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Affiliation(s)
- Ren-Jie Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Su-Fang Meng
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
| | - Xiao-Jiang Zheng
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- College of Life Sciences, Northwest University, Xi'an, China
| | - Bin Zhang
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
- College of Life Sciences, Northwest University, Xi'an, China
| | - Yang Yang
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
| | - Chao Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- College of Life Sciences, Northwest University, Xi'an, China
| | - Ai-Gen Fu
- College of Life Sciences, Northwest University, Xi'an, China
| | - Fu-Geng Zhao
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
| | - Wen-Zhi Lan
- Nanjing University-Nanjing Forestry University Joint Institute for Plant Molecular Biology, State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China.
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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14
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Funato Y, Miki H. The emerging roles and therapeutic potential of cyclin M/CorC family of Mg 2+ transporters. J Pharmacol Sci 2021; 148:14-18. [PMID: 34924118 DOI: 10.1016/j.jphs.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/01/2021] [Accepted: 09/10/2021] [Indexed: 11/15/2022] Open
Abstract
Cyclin M (CNNM) and its prokaryotic ortholog CorC belong to a family of proteins that function as Mg2+-extruding transporters by stimulating Na+/Mg2+ exchange, and thereby control intracellular Mg2+ levels. The Mg2+-extruding function of CNNM is inhibited by the direct binding of an oncogenic protein, phosphatase of regenerating liver (PRL), and this inhibition is responsible for the PRL-driven malignant progression of cancers. Studies with mouse strains deficient for the CNNM gene family revealed the importance of CNNM4 and CNNM2 in maintaining organismal Mg2+ homeostasis by participating in intestinal Mg2+ absorption and renal reabsorption, respectively. Moreover, CNNM proteins are involved in various diseases, and gene mutations in CNNM2 and CNNM4 cause dominant familial hypomagnesemia and Jalili syndrome, respectively. Genome wide association studies have also revealed the importance of CNNM2 in multiple major diseases, such as hypertension and schizophrenia. Collectively, the molecular and biological characterizations of CNNM/CorC show that they are an intriguing therapeutic target; the current status of drug development targeting these proteins is also discussed.
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Affiliation(s)
- 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; Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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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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Iwadate Y, Ramezanifard R, Golubeva YA, Fenlon LA, Slauch JM. PaeA (YtfL) protects from cadaverine and putrescine stress in Salmonella Typhimurium and E. coli. Mol Microbiol 2021; 115:1379-1394. [PMID: 33481283 PMCID: PMC10923242 DOI: 10.1111/mmi.14686] [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: 11/11/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Salmonella and E. coli synthesize, import, and export cadaverine, putrescine, and spermidine to maintain physiological levels and provide pH homeostasis. Both low and high intracellular levels of polyamines confer pleiotropic phenotypes or lethality. Here, we demonstrate that the previously uncharacterized inner membrane protein PaeA (YtfL) is required for reducing cytoplasmic cadaverine and putrescine concentrations. We identified paeA as a gene involved in stationary phase survival when cells were initially grown in acidic medium, in which they produce cadaverine. The paeA mutant is also sensitive to putrescine, but not to spermidine or spermine. Sensitivity to external cadaverine in stationary phase is only observed at pH > 8, suggesting that the polyamines need to be deprotonated to passively diffuse into the cell cytoplasm. In the absence of PaeA, intracellular polyamine levels increase and the cells lose viability. Degradation or modification of the polyamines is not relevant. Ectopic expression of the known cadaverine exporter, CadB, in stationary phase partially suppresses the paeA phenotype, and overexpression of PaeA in exponential phase partially complements a cadB mutant grown in acidic medium. These data support the hypothesis that PaeA is a cadaverine/putrescine exporter, reducing potentially toxic levels under certain stress conditions.
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Affiliation(s)
- Yumi Iwadate
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Rouhallah Ramezanifard
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Yekaterina A. Golubeva
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Luke A. Fenlon
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
- Current address: Department of Internal Medicine, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City, Utah 84132
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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17
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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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18
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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: 34] [Impact Index Per Article: 11.3] [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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19
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Khemici V, Prados J, Petrignani B, Di Nolfi B, Bergé E, Manzano C, Giraud C, Linder P. The DEAD-box RNA helicase CshA is required for fatty acid homeostasis in Staphylococcus aureus. PLoS Genet 2020; 16:e1008779. [PMID: 32730248 PMCID: PMC7392221 DOI: 10.1371/journal.pgen.1008779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/15/2020] [Indexed: 01/05/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that can grow in a wide array of conditions: on abiotic surfaces, on the skin, in the nose, in planktonic or biofilm forms and can cause many type of infections. Consequently, S. aureus must be able to adapt rapidly to these changing growth conditions, an ability largely driven at the posttranscriptional level. RNA helicases of the DEAD-box family play an important part in this process. In particular, CshA, which is part of the degradosome, is required for the rapid turnover of certain mRNAs and its deletion results in cold-sensitivity. To understand the molecular basis of this phenotype, we conducted a large genetic screen isolating 82 independent suppressors of cold growth. Full genome sequencing revealed the fatty acid synthesis pathway affected in many suppressor strains. Consistent with that result, sublethal doses of triclosan, a FASII inhibitor, can partially restore growth of a cshA mutant in the cold. Overexpression of the genes involved in branched-chain fatty acid synthesis was also able to suppress the cold-sensitivity. Using gas chromatography analysis of fatty acids, we observed an imbalance of straight and branched-chain fatty acids in the cshA mutant, compared to the wild-type. This imbalance is compensated in the suppressor strains. Thus, we reveal for the first time that the cold sensitive growth phenotype of a DEAD-box mutant can be explained, at least partially, by an improper membrane composition. The defect correlates with an accumulation of the pyruvate dehydrogenase complex mRNA, which is inefficiently degraded in absence of CshA. We propose that the resulting accumulation of acetyl-CoA fuels straight-chained fatty acid production at the expense of the branched ones. Strikingly, addition of acetate into the medium mimics the cshA deletion phenotype, resulting in cold sensitivity suppressed by the mutations found in our genetic screen or by sublethal doses of triclosan. DEAD-box RNA helicases are highly conserved proteins found in all domains of life. By acting on RNA secondary structures they determine the fate of RNA from transcription to degradation. Bacterial DEAD-box RNA helicases are not essential under laboratory conditions but are required for fitness and under stress conditions. Whereas many DEAD-box protein mutants display a cold sensitive phenotype, the underlying mechanisms have been studied only in few cases and found to be associated with ribosome biogenesis. We aimed here to elucidate the cold sensitivity of a cshA mutant in the Gram-positive opportunist pathogen Staphylococcus aureus. Our study revealed for the first time that part of the cold sensitivity is related to the inability of the bacterium to adapt the cytoplasmic membrane to lower temperatures. We propose that straight-chain fatty acid synthesis, reduced to sustain growth at lower temperature, is maintained due to inefficient turn-over of the pyruvate dehydrogenase mRNA, leading to elevated acetyl-CoA levels. This study allowed us to unravel at least in part the cold sensitive phenotype and to show that the pyruvate dehydrogenase activity plays an important function in the regulation of fatty acid composition of the membrane, a process that remains poorly understood in Gram-positive bacteria.
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Affiliation(s)
- Vanessa Khemici
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Bianca Petrignani
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Di Nolfi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Elodie Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Caroline Giraud
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
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20
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Hashizume O, Funato Y, Yamazaki D, Miki H. Excessive Mg 2+ Impairs Intestinal Homeostasis by Enhanced Production of Adenosine Triphosphate and Reactive Oxygen Species. Antioxid Redox Signal 2020; 33:20-34. [PMID: 32148064 DOI: 10.1089/ars.2019.7951] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aims: Mg2+ is fundamental for life, and its shortage severely impairs vital functions. However, whether excessive Mg2+ has beneficial or adverse effects has remained unknown. To clarify this issue, we analyzed the effect of suppressing the functions of Cyclin M (CNNM) Mg2+ efflux transporters in various experimental systems. Results: Investigation of short-lived Caenorhabditis elegans worms mutated for CNNM genes revealed reactive oxygen species (ROS) augmentation in intestinal cells, coincidently with high levels of Mg2+. Knockdown of gtl-1, encoding Mg2+-incorporating channel into intestinal cells, reduced ROS levels and restored life span, confirming the causative role of excessive Mg2+. Also, inactivation of orthologous CNNM in human cultured cells and mice by RNA interference, expression of CNNM-inhibiting protein, phosphatase of regenerating liver 3, or gene knockout resulted in ROS overproduction. Moreover, biochemical analyses revealed that excessive Mg2+ stimulates adenosine triphosphate overproduction and accelerates mitochondrial electron transport, whose suppression shut down ROS generation. Innovation and Conclusion: These results provide definitive evidence that excessive Mg2+ drives overproduction of ROS by affecting energy metabolism, implying the crucial importance of the tight regulation of intracellular Mg2+ levels.
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Affiliation(s)
- Osamu Hashizume
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Daisuke Yamazaki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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21
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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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22
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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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23
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Bacillus subtilis TerC Family Proteins Help Prevent Manganese Intoxication. J Bacteriol 2020; 202:JB.00624-19. [PMID: 31685536 DOI: 10.1128/jb.00624-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/29/2019] [Indexed: 12/24/2022] Open
Abstract
Manganese (Mn) is an essential element and is required for the virulence of many pathogens. In Bacillus subtilis, Mn(II) homeostasis is regulated by MntR, a Mn(II)-responsive, DNA-binding protein. MntR serves as both a repressor of Mn(II) uptake transporters and as a transcriptional activator for expression of two cation diffusion facilitator Mn(II) efflux pumps, MneP and MneS. Mutants lacking either mntR or both mneP and mneS are extremely sensitive to Mn(II) intoxication. Using transposon mutagenesis to select suppressors of Mn(II) sensitivity, we identified YceF, a TerC family membrane protein, as capable of providing Mn(II) resistance. Another TerC paralog, YkoY, is regulated by a Mn(II)-sensing riboswitch and is partially redundant in function with YceF. YkoY is regulated in parallel with an unknown function protein YybP, also controlled by a Mn(II)-sensing riboswitch. Strains lacking between one and five of these known or putative Mn(II) tolerance proteins (MneP, MneS, YceF, YkoY, and YybP) were tested for sensitivity to Mn(II) in growth assays and for accumulation of Mn(II) using inductively coupled plasma mass spectrometry. Loss of YceF and, to a lesser extent, YkoY, sensitizes cells lacking the MneP and MneS efflux transporters to Mn(II) intoxication. This sensitivity correlates with elevated intracellular Mn(II), consistent with the suggestion that TerC proteins function in Mn(II) efflux.IMPORTANCE Manganese homeostasis is primarily regulated at the level of transport. Bacillus subtilis MntR serves as a Mn(II)-activated repressor of importer genes (mntH and mntABC) and an activator of efflux genes (mneP and mneS). Elevated intracellular Mn(II) also binds to Mn-sensing riboswitches to activate transcription of yybP and ykoY, which encodes a TerC family member. Here, we demonstrate that two TerC family proteins, YceF and YkoY, help prevent Mn(II) intoxication. TerC family proteins are widespread in bacteria and may influence host-pathogen interactions, but their effects on Mn(II) homeostasis are unclear. Our results suggest that TerC proteins work by Mn(II) export under Mn(II) overload conditions to help alleviate toxicity.
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24
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Giménez-Mascarell P, Oyenarte I, González-Recio I, Fernández-Rodríguez C, Corral-Rodríguez MÁ, Campos-Zarraga I, Simón J, Kostantin E, Hardy S, Díaz Quintana A, Zubillaga Lizeaga M, Merino N, Diercks T, Blanco FJ, Díaz Moreno I, Martínez-Chantar ML, Tremblay ML, Müller D, Siliqi D, Martínez-Cruz LA. Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4. Int J Mol Sci 2019; 20:E6279. [PMID: 31842432 PMCID: PMC6940986 DOI: 10.3390/ijms20246279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
The four member family of "Cyclin and Cystathionine β-synthase (CBS) domain divalent metal cation transport mediators", CNNMs, are the least-studied mammalian magnesium transport mediators. CNNM4 is abundant in the brain and the intestinal tract, and its abnormal activity causes Jalili Syndrome. Recent findings show that suppression of CNNM4 in mice promotes malignant progression of intestinal polyps and is linked to infertility. The association of CNNM4 with phosphatases of the regenerating liver, PRLs, abrogates its Mg2+-efflux capacity, thus resulting in an increased intracellular Mg2+ concentration that favors tumor growth. Here we present the crystal structures of the two independent intracellular domains of human CNNM4, i.e., the Bateman module and the cyclic nucleotide binding-like domain (cNMP). We also derive a model structure for the full intracellular region in the absence and presence of MgATP and the oncogenic interacting partner, PRL-1. We find that only the Bateman module interacts with ATP and Mg2+, at non-overlapping sites facilitating their positive cooperativity. Furthermore, both domains dimerize autonomously, where the cNMP domain dimer forms a rigid cleft to restrict the Mg2+ induced sliding of the inserting CBS1 motives of the Bateman module, from a twisted to a flat disk shaped dimer.
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Grants
- ETORTEK IE05-147 Departamento de Industria, Innovación, Comercio y Turismo del Gobierno Vasco
- IE07-202 Departamento de Industria, Innovación, Comercio y Turismo del Gobierno Vasco
- 7/13/08/2006/11 Diputación Foral de Bizkaia
- 7/13/08/2005/14 Diputación Foral de Bizkaia
- BFU2010-17857 Ministerio de Ciencia e Innovación
- BFU2013-47531-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BES-2014-068464 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BFU2016-77408-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BES-2017-080435 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- CSD2008-00005 MICINN CONSOLIDER-INGENIO 2010 Program
- BAG MX20113 Diamond Light source
- 2013111114 Gobierno Vasco-Departamento de Salud
- SAF2017-87301-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO15/CA/014 EITB Maratoia
- SEV-2016-0644 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- 12.01.134/2bT4 Berlin Institute of Health
- #343439 Canadian Institute for Health Research
- MX15832-9 Diamond Light Source
- MX15832-10 Diamond Light Source
- PGC2018-096049-B100 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- CTQ2017-83810-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- PI2010-17 Departamento de Educación, Universidades e Investigación del Gobierno Vasco
- BAG 2019073624 ALBA Synchrotron
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Affiliation(s)
- Paula Giménez-Mascarell
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
| | - Iker Oyenarte
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
| | - Irene González-Recio
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
| | - Carmen Fernández-Rodríguez
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
| | - María Ángeles Corral-Rodríguez
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
| | - Igone Campos-Zarraga
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
| | - Jorge Simón
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
| | - Elie Kostantin
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; (E.K.); (S.H.); (M.L.T.)
| | - Serge Hardy
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; (E.K.); (S.H.); (M.L.T.)
| | - Antonio Díaz Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla—CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain; (A.D.Q.); (I.D.M.)
| | - Mara Zubillaga Lizeaga
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 800, 48160 Derio, Spain; (M.Z.L.); (N.M.); (T.D.); (F.J.B.)
| | - Nekane Merino
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 800, 48160 Derio, Spain; (M.Z.L.); (N.M.); (T.D.); (F.J.B.)
| | - Tammo Diercks
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 800, 48160 Derio, Spain; (M.Z.L.); (N.M.); (T.D.); (F.J.B.)
| | - Francisco J. Blanco
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 800, 48160 Derio, Spain; (M.Z.L.); (N.M.); (T.D.); (F.J.B.)
- IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain
| | - Irene Díaz Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla—CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain; (A.D.Q.); (I.D.M.)
| | - María Luz Martínez-Chantar
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain
| | - Michel L. Tremblay
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; (E.K.); (S.H.); (M.L.T.)
| | - Dominik Müller
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Disorders, Charité Universitäts medizin, 13353 Berlin, Germany;
| | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche (CNR), Via G. Amendola 122/O, 70126 Bari, Italy;
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 801A, 48160 Derio, Spain; (P.G.-M.); (I.O.); (I.G.-R.); (C.F.-R.); (M.Á.C.-R.); (I.C.-Z.); (J.S.); (M.L.M.-C.)
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25
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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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26
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Trachsel E, Redder P, Linder P, Armitano J. Genetic screens reveal novel major and minor players in magnesium homeostasis of Staphylococcus aureus. PLoS Genet 2019; 15:e1008336. [PMID: 31415562 PMCID: PMC6711546 DOI: 10.1371/journal.pgen.1008336] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/27/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022] Open
Abstract
Magnesium is one of the most abundant metal ions in living cells. Very specific and devoted transporters have evolved for transporting Mg2+ ions across the membrane and maintain magnesium homeostasis. Using genetic screens, we were able to identify the main players in magnesium homeostasis in the opportunistic pathogen Staphylococcus aureus. Here, we show that import of magnesium relies on the redundant activity of either CorA2 or MgtE since in absence of these two importers, bacteria require increased amounts of magnesium in the medium. A third CorA-like importer seems to play a minor role, at least under laboratory conditions. For export of magnesium, we identified two proteins, MpfA and MpfB. MpfA, is the main actor since it is essential for growth in high magnesium concentrations. We show that gain of function mutations or overexpression of the minor factor, MpfB, which is part of a sigmaB controlled stress response regulon, can compensate for the absence of MpfA.
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Affiliation(s)
- Emilie Trachsel
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Redder
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- LMGM UMR5100, Centre de Biologie Integrative, Paul Sabatier University, Toulouse, France
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Joshua Armitano
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
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27
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Schuster CF, Howard SA, Gründling A. Use of the counter selectable marker PheS* for genome engineering in Staphylococcus aureus. Microbiology (Reading) 2019; 165:572-584. [DOI: 10.1099/mic.0.000791] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Christopher F. Schuster
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Sophie A. Howard
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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28
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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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29
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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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Current Structural Knowledge on the CNNM Family of Magnesium Transport Mediators. Int J Mol Sci 2019; 20:ijms20051135. [PMID: 30845649 PMCID: PMC6429129 DOI: 10.3390/ijms20051135] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
The cyclin and cystathionine β-synthase (CBS) domain magnesium transport mediators, CNNMs, are key players in maintaining the homeostasis of magnesium in different organs. The human family includes four members, whose impaired activity causes diseases such as Jalili Syndrome or Familial Hypomagnesemia, but is also linked to neuropathologic disorders, altered blood pressure, and infertility. Recent findings demonstrated that CNNMs are associated with the highly oncogenic phosphatases of the regenerating liver to promote tumor growth and metastasis, which has attracted renewed focus on their potential exploitation as targets for cancer treatment. However, the exact function of CNNMs remains unclear and is subject to debate, proposed as either direct transporters, sensors, or homeostatic factors. This review gathers the current structural knowledge on the CNNM family, highlighting similarities and differences with the closely related structural partners such as the bacterial Mg2+/Co2+ efflux protein CorC and the Mg2+ channel MgtE.
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Molecular function and biological importance of CNNM family Mg2+ transporters. J Biochem 2018; 165:219-225. [DOI: 10.1093/jb/mvy095] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
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Le Scornet A, Redder P. Post-transcriptional control of virulence gene expression in Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:734-741. [PMID: 29705591 DOI: 10.1016/j.bbagrm.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 12/12/2022]
Abstract
Opportunistic pathogens have to be ready to change life-style whenever the occasion arises, and therefore need to keep tight control over the expression of their virulence factors. Doubly so for commensal bacteria, such as Staphylococcus aureus, which should avoid harming their hosts when they are in a state of peaceful co-existence. S. aureus carries very few sigma factors to help define the transcriptional programs, but instead uses a plethora of small RNA molecules and RNA-RNA interactions to regulate gene expression post-transcriptionally. The endoribonucleases RNase III and RNase Y contribute to this regulatory diversity, and provide a link to RNA-decay and intra-cellular spatiotemporal control of expression. In this review we describe some of these post-transcriptional mechanisms as well as some of the novel transcriptomic approaches that have been used to find and to study them.
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Affiliation(s)
- Alexandre Le Scornet
- LMGM, Centre de Biologie Integrative, Paul Sabatier University, 118, Route de Narbonne, 31062 Toulouse, France
| | - Peter Redder
- LMGM, Centre de Biologie Integrative, Paul Sabatier University, 118, Route de Narbonne, 31062 Toulouse, France.
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Funato Y, Furutani K, Kurachi Y, Miki H. CrossTalk proposal: CNNM proteins are Na + /Mg 2+ exchangers playing a central role in transepithelial Mg 2+ (re)absorption. J Physiol 2018; 596:743-746. [PMID: 29383719 DOI: 10.1113/jp275248] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuharu Furutani
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, USA
| | - Yoshihisa Kurachi
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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