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Felix J, Bumba L, Liesche C, Fraudeau A, Rébeillé F, El Khoury JY, Huard K, Gallet B, Moriscot C, Kleman JP, Duhoo Y, Jessop M, Kandiah E, Barras F, Jouhet J, Gutsche I. The AAA+ ATPase RavA and its binding partner ViaA modulate E. coli aminoglycoside sensitivity through interaction with the inner membrane. Nat Commun 2022; 13:5502. [PMID: 36127320 PMCID: PMC9489729 DOI: 10.1038/s41467-022-32992-9] [Citation(s) in RCA: 4] [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: 03/01/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
Enteric bacteria have to adapt to environmental stresses in the human gastrointestinal tract such as acid and nutrient stress, oxygen limitation and exposure to antibiotics. Membrane lipid composition has recently emerged as a key factor for stress adaptation. The E. coli ravA-viaA operon is essential for aminoglycoside bactericidal activity under anaerobiosis but its mechanism of action is unclear. Here we characterise the VWA domain-protein ViaA and its interaction with the AAA+ ATPase RavA, and find that both proteins localise at the inner cell membrane. We demonstrate that RavA and ViaA target specific phospholipids and subsequently identify their lipid-binding sites. We further show that mutations abolishing interaction with lipids restore induced changes in cell membrane morphology and lipid composition. Finally we reveal that these mutations render E. coli gentamicin-resistant under fumarate respiration conditions. Our work thus uncovers a ravA-viaA-based pathway which is mobilised in response to aminoglycosides under anaerobiosis and engaged in cell membrane regulation.
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Affiliation(s)
- Jan Felix
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ladislav Bumba
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Institute of Microbiology, The Academy of Sciences of the Czech Republic, Videnska, 1083, Prague, Czech Republic
| | - Clarissa Liesche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Angélique Fraudeau
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- EMBL Grenoble, 71 Avenue des martyrs, Grenoble, France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Univ Grenoble Alpes, CEA, CNRS, INRAE, IRIG, 17 Avenue des martyrs, Grenoble, France
| | - Jessica Y El Khoury
- Institut Pasteur, Université de Paris, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, Paris, France
| | - Karine Huard
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Benoit Gallet
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Christine Moriscot
- Univ Grenoble Alpes, CEA, CNRS, ISBG, 71 Avenue des martyrs, Grenoble, France
| | - Jean-Philippe Kleman
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Yoan Duhoo
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Matthew Jessop
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Eaazhisai Kandiah
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des martyrs, Grenoble, France
| | - Frédéric Barras
- Institut Pasteur, Université de Paris, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, Paris, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Univ Grenoble Alpes, CEA, CNRS, INRAE, IRIG, 17 Avenue des martyrs, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France.
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Bhandari V, Van Ommen DAJ, Wong KS, Houry WA. Analysis of the Evolution of the MoxR ATPases. J Phys Chem A 2022; 126:4734-4746. [PMID: 35852937 DOI: 10.1021/acs.jpca.2c02554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MoxR proteins comprise a family of ATPases Associated with diverse cellular Activities (AAA+). These proteins are widespread and found across the diversity of prokaryotic species. Despite their ubiquity, members of the group remain poorly characterized. Only a few examples of MoxR proteins have been associated with cellular roles, where they have been shown to perform chaperone-like functions. A characteristic feature of MoxR proteins is their association with proteins containing the von Willebrand factor type A (VWA) domain. In an effort to understand the spread and diversity of the MoxR family, an evolutionary approach was undertaken. Phylogenetic techniques were used to define nine major subfamilies within the MoxR family. A combination of phylogenetic and genomic approaches was utilized to explore the extent of the partnership between the MoxR and VWA domain containing proteins (VWA proteins). These analyses led to the clarification of genetic linkages between MoxR and VWA proteins. A significant partnership is described here, as seven of nine MoxR subfamilies were found to be linked to VWA proteins. Available genomic data were also used to assess the intraprotein diversification of MoxR and VWA protein sequences. Data clearly indicated that, in MoxR proteins, the ATPase domain is maintained with high conservation while the remaining protein sequence evolves at a faster rate; a similar pattern was observed for the VWA domain in VWA proteins. Overall, our data present insights into the modular evolution of MoxR ATPases.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - David A J Van Ommen
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Keith S Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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Huang Y, Ji X, Ma Z, Łężyk M, Xue Y, Zhao H. Green chemical and biological synthesis of cadaverine: recent development and challenges. RSC Adv 2021; 11:23922-23942. [PMID: 35479032 PMCID: PMC9036910 DOI: 10.1039/d1ra02764f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/29/2021] [Indexed: 11/21/2022] Open
Abstract
Cadaverine has great potential to be used as an important monomer for the development of a series of high value-added products with market prospects. The most promising strategies for cadaverine synthesis involve using green chemical and bioconversion technologies. Herein, the review focuses on the progress and strategies towards the green chemical synthesis and biosynthesis of cadaverine. Specifically, we address the specific biosynthetic pathways of cadaverine from different substrates as well as extensively discussing the origination, structure and catalytic mechanism of the key lysine decarboxylases. The advanced strategies for process intensification, the separation and purification of cadaverine have been summarized. Furthermore, the challenging issues of the environmental, economic, and applicable impact for cadaverine production are also highlighted. This review concludes with the promising outlooks of state-of-the-art applications of cadaverine along with some insights toward their challenges and potential improvements.
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Affiliation(s)
- Yuhong Huang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China
- Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China
- Zhongke Langfang Institute of Process Engineering Langfang 065001 China
| | - Xiuling Ji
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Zhanling Ma
- Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China
| | - Mateusz Łężyk
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology Berdychowo 4 60-965 Poznan Poland
| | - Yaju Xue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Hai Zhao
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China
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Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance. Sci Rep 2021; 11:972. [PMID: 33441661 PMCID: PMC7806604 DOI: 10.1038/s41598-020-79611-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Francisella tularensis is one of the most virulent pathogenic bacteria causing the acute human respiratory disease tularemia. While the mechanisms underlying F. tularensis pathogenesis are largely unknown, previous studies have shown that a F. novicida transposon mutant with insertions in a gene coding for a putative lysine decarboxylase was attenuated in mouse spleen, suggesting a possible role of its protein product as a virulence factor. Therefore, we set out to structurally and functionally characterize the F. novicida lysine decarboxylase, which we termed LdcF. Here, we investigate the genetic environment of ldcF as well as its evolutionary relationships with other basic AAT-fold amino acid decarboxylase superfamily members, known as key actors in bacterial adaptative stress response and polyamine biosynthesis. We determine the crystal structure of LdcF and compare it with the most thoroughly studied lysine decarboxylase, E. coli LdcI. We analyze the influence of ldcF deletion on bacterial growth under different stress conditions in dedicated growth media, as well as in infected macrophages, and demonstrate its involvement in oxidative stress resistance. Finally, our mass spectrometry-based quantitative proteomic analysis enables identification of 80 proteins with expression levels significantly affected by ldcF deletion, including several DNA repair proteins potentially involved in the diminished capacity of the F. novicida mutant to deal with oxidative stress. Taken together, we uncover an important role of LdcF in F. novicida survival in host cells through participation in oxidative stress response, thereby singling out this previously uncharacterized protein as a potential drug target.
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Abstract
Bacteria possess a sophisticated arsenal of defense mechanisms that allow them to survive in adverse conditions. Adaptation to acid stress and hypoxia is crucial for the enterobacterial transmission in the gastrointestinal tract of their human host. When subjected to low pH, Escherichia coli and many other enterobacteria activate a proton-consuming resistance system based on the acid stress-inducible lysine decarboxylase LdcI. Here we develop generally applicable tools to uncover the spatial localization of LdcI inside the cell by superresolution fluorescence microscopy and investigate the in vitro supramolecular organization of this enzyme by cryo-EM. We build on these results to propose a mechanistic model for LdcI function and offer tools for further in vivo investigations. Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid stress-response regulation of Escherichia coli LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localization of nanobody-labeled endogenous wild-type LdcI in acid-stressed E. coli cells and show that it organizes into distinct patches at the cell periphery. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerization as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-EM and reveal the molecular determinants of LdcI polymerization, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organization in the acid stress response.
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Jessop M, Arragain B, Miras R, Fraudeau A, Huard K, Bacia-Verloop M, Catty P, Felix J, Malet H, Gutsche I. Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex. Commun Biol 2020; 3:46. [PMID: 31992852 PMCID: PMC6987120 DOI: 10.1038/s42003-020-0772-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/11/2020] [Indexed: 01/13/2023] Open
Abstract
The hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI form a 3.3 MDa cage, proposed to assist assembly of specific respiratory complexes in E. coli. Here, we show that inside the LdcI-RavA cage, RavA hexamers adopt an asymmetric spiral conformation in which the nucleotide-free seam is constrained to two opposite orientations. Cryo-EM reconstructions of free RavA reveal two co-existing structural states: an asymmetric spiral, and a flat C2-symmetric closed ring characterised by two nucleotide-free seams. The closed ring RavA state bears close structural similarity to the pseudo two-fold symmetric crystal structure of the AAA+ unfoldase ClpX, suggesting a common ATPase mechanism. Based on these structures, and in light of the current knowledge regarding AAA+ ATPases, we propose different scenarios for the ATP hydrolysis cycle of free RavA and the LdcI-RavA cage-like complex, and extend the comparison to other AAA+ ATPases of clade 7.
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Affiliation(s)
- Matthew Jessop
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Benoit Arragain
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Roger Miras
- Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, CEA, CNRS, DRF, IRIG, UMR 5249, 17 rue des Martyrs, F-38054, Grenoble, France
| | - Angélique Fraudeau
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Karine Huard
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Patrice Catty
- Laboratoire de Chimie et Biologie des Métaux, Univ. Grenoble Alpes, CEA, CNRS, DRF, IRIG, UMR 5249, 17 rue des Martyrs, F-38054, Grenoble, France
| | - Jan Felix
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
| | - Hélène Malet
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
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Kandiah E, Carriel D, Garcia PS, Felix J, Banzhaf M, Kritikos G, Bacia-Verloop M, Brochier-Armanet C, Elsen S, Gutsche I. Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA. Structure 2019; 27:1842-1854.e4. [PMID: 31653338 DOI: 10.1016/j.str.2019.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/09/2019] [Accepted: 10/01/2019] [Indexed: 11/28/2022]
Abstract
The only enzyme responsible for cadaverine production in the major multidrug-resistant human pathogen Pseudomonas aeruginosa is the lysine decarboxylase LdcA. This enzyme modulates the general polyamine homeostasis, promotes growth, and reduces bacterial persistence during carbenicillin treatment. Here we present a 3.7-Å resolution cryoelectron microscopy structure of LdcA. We introduce an original approach correlating phylogenetic signal with structural information and reveal possible recombination among LdcA and arginine decarboxylase subfamilies within structural domain boundaries. We show that LdcA is involved in full virulence in an insect pathogenesis model. Furthermore, unlike its enterobacterial counterparts, LdcA is regulated neither by the stringent response alarmone ppGpp nor by the AAA+ ATPase RavA. Instead, the P. aeruginosa ravA gene seems to play a defensive role. Altogether, our study identifies LdcA as an important player in P. aeruginosa physiology and virulence and as a potential drug target.
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Affiliation(s)
- Eaazhisai Kandiah
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Diego Carriel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Pierre Simon Garcia
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Jan Felix
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Manuel Banzhaf
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - George Kritikos
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France; MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 Passage du Vercors, 69367 Lyon Cedex 07, France
| | - Sylvie Elsen
- Biology of Cancer and Infection, U1036 INSERM, CEA, University of Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Irina Gutsche
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
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Kampinga HH, Mayer MP, Mogk A. Protein quality control: from mechanism to disease : EMBO Workshop, Costa de la Calma (Mallorca), Spain, April 28 - May 03, 2019. Cell Stress Chaperones 2019; 24:1013-1026. [PMID: 31713048 PMCID: PMC6882752 DOI: 10.1007/s12192-019-01040-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
The cellular protein quality control machinery with its central constituents of chaperones and proteases is vital to maintain protein homeostasis under physiological conditions and to protect against acute stress conditions. Imbalances in protein homeostasis also are keys to a plethora of genetic and acquired, often age-related, diseases as well as aging in general. At the EMBO Workshop, speakers covered all major aspects of cellular protein quality control, from basic mechanisms at the molecular, cellular, and organismal level to medical translation. In this report, the highlights of the meeting will be summarized.
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Affiliation(s)
- Harm H Kampinga
- Department of Biomedical Science of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Matthias P Mayer
- Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
| | - Axel Mogk
- Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
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9
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Carriel D, Simon Garcia P, Castelli F, Lamourette P, Fenaille F, Brochier-Armanet C, Elsen S, Gutsche I. A Novel Subfamily of Bacterial AAT-Fold Basic Amino Acid Decarboxylases and Functional Characterization of Its First Representative: Pseudomonas aeruginosa LdcA. Genome Biol Evol 2018; 10:3058-3075. [PMID: 30321344 PMCID: PMC6257575 DOI: 10.1093/gbe/evy228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
Polyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by pyridoxal-5-phosphate-dependent amino acid decarboxylases referred to as Lysine-Arginine-Ornithine decarboxylases (LAOdcs). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancient nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria. We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral in Betaproteobacteria and Pseudomonadaceae. We analyzed the expression of LdcA from Pseudomonas aeruginosa, and uncovered its role, intimately linked to cadaverine (Cad) production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines—Cad, putrescine (Put), and spermidine (Spd)—in P. aeruginosa by demonstrating the link between their intracellular level, as well as the capacity of Put and Spd to complement the growth phenotype of the ldcA mutant.
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Affiliation(s)
- Diego Carriel
- University of Grenoble Alpes, CNRS, CEA, CNRS, IBS, France.,University of Grenoble Alpes, INSERM, CEA, ERL5261 CNRS, BIG BCI, France
| | - Pierre Simon Garcia
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France.,MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines, Lyon, France
| | - Florence Castelli
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, France
| | - Patricia Lamourette
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, France
| | - François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France.,MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines, Lyon, France
| | - Sylvie Elsen
- University of Grenoble Alpes, INSERM, CEA, ERL5261 CNRS, BIG BCI, France
| | - Irina Gutsche
- University of Grenoble Alpes, CNRS, CEA, CNRS, IBS, France
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Deng J, Gao H, Gao Z, Zhao H, Yang Y, Wu Q, Wu B, Jiang C. Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms. PLoS One 2017; 12:e0185060. [PMID: 28931053 PMCID: PMC5607190 DOI: 10.1371/journal.pone.0185060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/06/2017] [Indexed: 11/18/2022] Open
Abstract
L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs. Multiple sequence alignment analysis revealed that Ldc1E contained a highly conserved motif Ser-X-His-Lys (Pxl), and molecular docking results showed that this motif was located in the active site and could combine with the cofactor pyridoxal 5'-phosphate. The ldc1E gene was subcloned into the pET-30a(+) vector and highly expressed in Escherichia coli BL21 (DE3) pLysS. The recombinant protein was purified to homogeneity. The maximum activity of Ldc1E occurred at pH 6.5 and 40°C using L-lysine monohydrochloride as the substrate. Recombinant Ldc1E had apparent Km, kcat, and kcat/Km values of 1.08±0.16 mM, 5.09±0.63 s-1, and 4.73×103 s-1 M-1, respectively. The specific activity of Ldc1E was 1.53±0.06 U mg-1 protein. Identifying a metagenome-derived LDC gene provided a rational reference for further gene modifications in industrial applications.
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Affiliation(s)
- Jie Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Hua Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Zhen Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Huaxian Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Ying Yang
- College of Ocean and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, China
| | - Qiaofen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Bo Wu
- College of Ocean and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
- * E-mail:
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11
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Li P, Vermeulen NA, Malliakas CD, Gómez-Gualdrón DA, Howarth AJ, Mehdi BL, Dohnalkova A, Browning ND, O’Keeffe M, Farha OK. Bottom-up construction of a superstructure in a porous uranium-organic crystal. Science 2017; 356:624-627. [DOI: 10.1126/science.aam7851] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/10/2017] [Indexed: 01/20/2023]
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12
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Wong KS, Bhandari V, Janga SC, Houry WA. The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex. J Mol Biol 2017; 429:324-344. [DOI: 10.1016/j.jmb.2016.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 01/02/2023]
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13
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Chan SWS, Yau J, Ing C, Liu K, Farber P, Won A, Bhandari V, Kara-Yacoubian N, Seraphim TV, Chakrabarti N, Kay LE, Yip CM, Pomès R, Sharpe S, Houry WA. Mechanism of Amyloidogenesis of a Bacterial AAA+ Chaperone. Structure 2016; 24:1095-109. [PMID: 27265850 DOI: 10.1016/j.str.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/27/2016] [Accepted: 05/01/2016] [Indexed: 10/21/2022]
Abstract
Amyloids are fibrillar protein superstructures that are commonly associated with diseases in humans and with physiological functions in various organisms. The precise mechanisms of amyloid formation remain to be elucidated. Surprisingly, we discovered that a bacterial Escherichia coli chaperone-like ATPase, regulatory ATPase variant A (RavA), and specifically the LARA domain in RavA, forms amyloids under acidic conditions at elevated temperatures. RavA is involved in modulating the proper assembly of membrane respiratory complexes. LARA contains an N-terminal loop region followed by a β-sandwich-like folded core. Several approaches, including nuclear magnetic resonance spectroscopy and molecular dynamics simulations, were used to determine the mechanism by which LARA switches to an amyloid state. These studies revealed that the folded core of LARA is amyloidogenic and is protected by its N-terminal loop. At low pH and high temperatures, the interaction of the N-terminal loop with the folded core is disrupted, leading to amyloid formation.
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Affiliation(s)
- Sze Wah Samuel Chan
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Jason Yau
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Christopher Ing
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kaiyin Liu
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Patrick Farber
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Amy Won
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Nareg Kara-Yacoubian
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Nilmadhab Chakrabarti
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Simon Sharpe
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada.
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14
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Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA. Sci Rep 2016; 6:24601. [PMID: 27080013 PMCID: PMC4832331 DOI: 10.1038/srep24601] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress
response enzyme whereas LdcC is its close paralogue thought to play mainly a
metabolic role. A unique macromolecular cage formed by two decamers of the
Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown
to counteract acid stress under starvation. Previously, we proposed a pseudoatomic
model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal
structures of an inactive LdcI decamer and a RavA monomer. We now present
cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and
an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for
their enzymatic activity. Comparison with each other and with available structures
uncovers differences between LdcI and LdcC explaining why only the acid stress
response enzyme is capable of binding RavA. We identify interdomain movements
associated with the pH-dependent enzyme activation and with the RavA binding.
Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain
enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the
cage-like assembly with RavA, implying that this complex may have an important
function under particular stress conditions.
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15
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Ezraty B, Barras F. The ‘liaisons dangereuses’ between iron and antibiotics. FEMS Microbiol Rev 2016; 40:418-35. [DOI: 10.1093/femsre/fuw004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 12/15/2022] Open
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16
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Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proc Natl Acad Sci U S A 2015; 112:E4017-25. [PMID: 26170309 DOI: 10.1073/pnas.1500257112] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Members of the AAA family of ATPases assemble into hexameric double rings and perform vital functions, yet their molecular mechanisms remain poorly understood. Here, we report structures of the Pex1/Pex6 complex; mutations in these proteins frequently cause peroxisomal diseases. The structures were determined in the presence of different nucleotides by cryo-electron microscopy. Models were generated using a computational approach that combines Monte Carlo placement of structurally homologous domains into density maps with energy minimization and refinement protocols. Pex1 and Pex6 alternate in an unprecedented hexameric double ring. Each protein has two N-terminal domains, N1 and N2, structurally related to the single N domains in p97 and N-ethylmaleimide sensitive factor (NSF); N1 of Pex1 is mobile, but the others are packed against the double ring. The N-terminal ATPase domains are inactive, forming a symmetric D1 ring, whereas the C-terminal domains are active, likely in different nucleotide states, and form an asymmetric D2 ring. These results suggest how subunit activity is coordinated and indicate striking similarities between Pex1/Pex6 and p97, supporting the hypothesis that the Pex1/Pex6 complex has a role in peroxisomal protein import analogous to p97 in ER-associated protein degradation.
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