1
|
Christensen PM, Martin J, Uppuluri A, Joyce LR, Wei Y, Guan Z, Morcos F, Palmer KL. Lipid discovery enabled by sequence statistics and machine learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.12.562061. [PMID: 37873101 PMCID: PMC10592805 DOI: 10.1101/2023.10.12.562061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that Streptococcus agalactiae MprF synthesizes lysyl-phosphatidylglycerol (Lys-PG) from anionic PG, and a novel cationic lipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), from neutral glycolipid Glc-DAG. This unexpected result prompted us to investigate whether Lys-Glc-DAG occurs in other MprF-containing bacteria, and whether other novel MprF products exist. Here, we studied protein sequence features determining MprF substrate specificity. First, pairwise analyses identified several streptococcal MprFs synthesizing Lys-Glc-DAG. Second, a restricted Boltzmann machine-guided approach led us to discover an entirely new substrate for MprF in Enterococcus , diglucosyl-diacylglycerol (Glc2-DAG), and an expanded set of organisms that modify glycolipid substrates using MprF. Overall, we combined the wealth of available sequence data with machine learning to model evolutionary constraints on MprF sequences across the bacterial domain, thereby identifying a novel cationic lipid.
Collapse
|
2
|
Gill CP, Phan C, Platt V, Worrell D, Andl T, Roy H. The MprF homolog LysX synthesizes lysyl-diacylglycerol contributing to antibiotic resistance and virulence. Microbiol Spectr 2023; 11:e0142923. [PMID: 37768052 PMCID: PMC10580965 DOI: 10.1128/spectrum.01429-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/10/2023] [Indexed: 09/29/2023] Open
Abstract
Lysyl-diacylglycerol (Lys-DAG) was identified three decades ago in Mycobacterium phlei, but the biosynthetic pathway and function of this aminoacylated lipid have since remained uncharacterized. Combining genetic methods, mass spectrometry, and biochemical approaches, we show that the multiple peptide resistance factor (MprF) homolog LysX from Corynebacterium pseudotuberculosis and two mycobacterial species is responsible for Lys-DAG synthesis. LysX is conserved in most Actinobacteria and was previously implicated in the synthesis of another modified lipid, lysyl-phosphatidylglycerol (Lys-PG), in Mycobacterium tuberculosis. Although we detected low levels of Lys-PG in the membrane of C. pseudotuberculosis, our data suggest that Lys-PG is not directly synthesized by LysX and may require an additional downstream pathway, which is as yet undefined. Our results show that LysX in C. pseudotuberculosis is a major factor of resistance against a variety of positively charged antibacterial agents, including cationic antimicrobial peptides (e.g., human peptide LL-37 and polymyxin B) and aminoglycosides (e.g., gentamycin and apramycin). Deletion of lysX caused an increase in cellular membrane permeability without dissipation of the membrane potential, suggesting that loss of the protein does not result in mechanical damage to the cell membrane. Furthermore, lysX-deficient cells exhibited an attenuated virulence phenotype in a Galleria mellonella infection model, supporting a role for LysX during infection. Altogether, Lys-DAG represents a novel molecular determinant for antimicrobial resistance and virulence that may be widespread in Actinobacteria and points to a richer landscape than previously realized of lipid components contributing to overall membrane physiology in this important bacterial phylum. IMPORTANCE In the past two decades, tRNA-dependent modification of membrane phosphatidylglycerol has been implicated in altering the biochemical properties of the cell surface, thereby enhancing the antimicrobial resistance and virulence of various bacterial pathogens. Here, we show that in several Actinobacteria, the multifunctional protein LysX attaches lysine to diacylglycerol instead of phosphatidylglycerol. We found that lysyl-diacylglycerol (Lys-DAG) confers high levels of resistance against various cationic antimicrobial peptides and aminoglycosides and also enhances virulence. Our data show that Lys-DAG is a lipid commonly found in important actinobacterial pathogens, including Mycobacterium and Corynebacterium species.
Collapse
Affiliation(s)
- Cameron P. Gill
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Christopher Phan
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Vivien Platt
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Danielle Worrell
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Thomas Andl
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Hervé Roy
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| |
Collapse
|
3
|
Abeywansha T, Huang W, Ye X, Nawrocki A, Lan X, Jankowsky E, Taylor DJ, Zhang Y. The structural basis of tRNA recognition by arginyl-tRNA-protein transferase. Nat Commun 2023; 14:2232. [PMID: 37076488 PMCID: PMC10115844 DOI: 10.1038/s41467-023-38004-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.
Collapse
Affiliation(s)
- Thilini Abeywansha
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xuan Ye
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Allison Nawrocki
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xin Lan
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Derek J Taylor
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Yi Zhang
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| |
Collapse
|
4
|
Depleting Cationic Lipids Involved in Antimicrobial Resistance Drives Adaptive Lipid Remodeling in Enterococcus faecalis. mBio 2023; 14:e0307322. [PMID: 36629455 PMCID: PMC9973042 DOI: 10.1128/mbio.03073-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The bacterial cell membrane is an interface for cell envelope synthesis, protein secretion, virulence factor assembly, and a target for host cationic antimicrobial peptides (CAMPs). To resist CAMP killing, several Gram-positive pathogens encode the multiple peptide resistance factor (MprF) enzyme that covalently attaches cationic amino acids to anionic phospholipids in the cell membrane. While E. faecalis encodes two mprF paralogs, MprF2 plays a dominant role in conferring resistance to killing by the CAMP human β-defensin 2 (hBD-2) in E. faecalis strain OG1RF. The goal of the current study is to understand the broader lipidomic and functional roles of E. faecalis mprF. We analyzed the lipid profiles of parental wild-type and mprF mutant strains and show that while ΔmprF2 and ΔmprF1 ΔmprF2 mutants completely lacked cationic lysyl-phosphatidylglycerol (L-PG), the ΔmprF1 mutant synthesized ~70% of L-PG compared to the parent. Unexpectedly, we also observed a significant reduction of PG in ΔmprF2 and ΔmprF1 ΔmprF2. In the mprF mutants, particularly ΔmprF1 ΔmprF2, the decrease in L-PG and phosphatidylglycerol (PG) is compensated by an increase in a phosphorus-containing lipid, glycerophospho-diglucosyl-diacylglycerol (GPDGDAG), and D-ala-GPDGDAG. These changes were accompanied by a downregulation of de novo fatty acid biosynthesis and an accumulation of long-chain acyl-acyl carrier proteins (long-chain acyl-ACPs), suggesting that the suppression of fatty acid biosynthesis was mediated by the transcriptional repressor FabT. Growth in chemically defined media lacking fatty acids revealed severe growth defects in the ΔmprF1 ΔmprF2 mutant strain, but not the single mutants, which was partially rescued through supplementation with palmitic and stearic acids. Changes in lipid homeostasis correlated with lower membrane fluidity, impaired protein secretion, and increased biofilm formation in both ΔmprF2 and ΔmprF1 ΔmprF2, compared to the wild type and ΔmprF1. Collectively, our findings reveal a previously unappreciated role for mprF in global lipid regulation and cellular physiology, which could facilitate the development of novel therapeutics targeting MprF. IMPORTANCE The cell membrane plays a pivotal role in protecting bacteria against external threats, such as antibiotics. Cationic phospholipids such as lysyl-phosphatidyglycerol (L-PG) resist the action of cationic antimicrobial peptides through electrostatic repulsion. Here we demonstrate that L-PG depletion has several unexpected consequences in Enterococcus faecalis, including a reduction of phosphatidylglycerol (PG), enrichment of a phosphorus-containing lipid, reduced fatty acid synthesis accompanied by an accumulation of long-chain acyl-acyl carrier proteins (long chain acyl-ACPs), lower membrane fluidity, and impaired secretion. These changes are not deleterious to the organism as long as exogenous fatty acids are available for uptake from the culture medium. Our findings suggest an adaptive mechanism involving compensatory changes across the entire lipidome upon removal of a single phospholipid modification. Such adaptations must be considered when devising antimicrobial strategies that target membrane lipids.
Collapse
|
5
|
Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M. Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Nucleic Acids Res 2022; 50:11415-11425. [PMID: 36350642 PMCID: PMC9723616 DOI: 10.1093/nar/gkac1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Xenobiotic nucleic acids (XNAs) offer tremendous potential for synthetic biology, biotechnology, and molecular medicine but their ability to mimic nucleic acids still needs to be explored. Here, to study the ability of XNA oligonucleotides to mimic tRNA, we synthesized three L-Ala-tXNAs analogs. These molecules were used in a non-ribosomal peptide synthesis involving a bacterial Fem transferase. We compared the ability of this enzyme to use amino-acyl tXNAs containing 1',5'-anhydrohexitol (HNA), 2'-fluoro ribose (2'F-RNA) and 2'-fluoro arabinose. L-Ala-tXNA containing HNA or 2'F-RNA were substrates of the Fem enzyme. The synthesis of peptidyl-XNA and the resolution of their structures in complex with the enzyme show the impact of the XNA on protein binding. For the first time we describe functional tXNA in an in vitro assay. These results invite to test tXNA also as substitute for tRNA in translation.
Collapse
Affiliation(s)
| | | | - Guy Schepers
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Delphine Dorchêne
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, F-75006 Paris, France
| | - Laura Iannazzo
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay 91198, Gif-sur-Yvette, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Biomedical Research, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Mélanie Ethève-Quelquejeu
- Université Paris Cité, CNRS UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, F-75006Paris, France
| | | |
Collapse
|
6
|
Panda G, Dash S, Sahu SK. Harnessing the Role of Bacterial Plasma Membrane Modifications for the Development of Sustainable Membranotropic Phytotherapeutics. MEMBRANES 2022; 12:914. [PMID: 36295673 PMCID: PMC9612325 DOI: 10.3390/membranes12100914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Membrane-targeted molecules such as cationic antimicrobial peptides (CAMPs) are amongst the most advanced group of antibiotics used against drug-resistant bacteria due to their conserved and accessible targets. However, multi-drug-resistant bacteria alter their plasma membrane (PM) lipids, such as lipopolysaccharides (LPS) and phospholipids (PLs), to evade membrane-targeted antibiotics. Investigations reveal that in addition to LPS, the varying composition and spatiotemporal organization of PLs in the bacterial PM are currently being explored as novel drug targets. Additionally, PM proteins such as Mla complex, MPRF, Lpts, lipid II flippase, PL synthases, and PL flippases that maintain PM integrity are the most sought-after targets for development of new-generation drugs. However, most of their structural details and mechanism of action remains elusive. Exploration of the role of bacterial membrane lipidome and proteome in addition to their organization is the key to developing novel membrane-targeted antibiotics. In addition, membranotropic phytochemicals and their synthetic derivatives have gained attractiveness as popular herbal alternatives against bacterial multi-drug resistance. This review provides the current understanding on the role of bacterial PM components on multidrug resistance and their targeting with membranotropic phytochemicals.
Collapse
Affiliation(s)
- Gayatree Panda
- Department of Biotechnology, Maharaja Sriram Chandra Bhanjadeo University (Erstwhile: North Orissa University), Baripada 757003, India
| | - Sabyasachi Dash
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Santosh Kumar Sahu
- Department of Biotechnology, Maharaja Sriram Chandra Bhanjadeo University (Erstwhile: North Orissa University), Baripada 757003, India
| |
Collapse
|
7
|
Grob G, Hemmerle M, Yakobov N, Mahmoudi N, Fischer F, Senger B, Becker HD. tRNA-dependent addition of amino acids to cell wall and membrane components. Biochimie 2022; 203:93-105. [DOI: 10.1016/j.biochi.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
|
8
|
Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates. Proc Natl Acad Sci U S A 2022; 119:e2209597119. [PMID: 35878037 PMCID: PMC9351520 DOI: 10.1073/pnas.2209597119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNAArg as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNAArg, and a 3'-proximal segment of the tRNAArg moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe3+-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.
Collapse
|
9
|
Joyce LR, Manzer HS, da C. Mendonça J, Villarreal R, Nagao PE, Doran KS, Palmer KL, Guan Z. Identification of a novel cationic glycolipid in Streptococcus agalactiae that contributes to brain entry and meningitis. PLoS Biol 2022; 20:e3001555. [PMID: 35180210 PMCID: PMC8893666 DOI: 10.1371/journal.pbio.3001555] [Citation(s) in RCA: 2] [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: 10/05/2021] [Revised: 03/03/2022] [Accepted: 01/26/2022] [Indexed: 12/17/2022] Open
Abstract
Bacterial membrane lipids are critical for membrane bilayer formation, cell division, protein localization, stress responses, and pathogenesis. Despite their critical roles, membrane lipids have not been fully elucidated for many pathogens. Here, we report the discovery of a novel cationic glycolipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), which is synthesized in high abundance by the bacterium Streptococcus agalactiae (Group B Streptococcus, GBS). To our knowledge, Lys-Glc-DAG is more positively charged than any other known lipids. Lys-Glc-DAG carries 2 positive net charges per molecule, distinct from the widely described lysylated phospholipid lysyl-phosphatidylglycerol (Lys-PG) that carries one positive net charge due to the presence of a negatively charged phosphate moiety. We use normal phase liquid chromatography (NPLC) coupled with electrospray ionization (ESI) high-resolution tandem mass spectrometry (HRMS/MS) and genetic approaches to determine that Lys-Glc-DAG is synthesized by the enzyme MprF in GBS, which covalently modifies the neutral glycolipid Glc-DAG with the cationic amino acid lysine. GBS is a leading cause of neonatal meningitis, which requires traversal of the endothelial blood–brain barrier (BBB). We demonstrate that GBS strains lacking mprF exhibit a significant decrease in the ability to invade BBB endothelial cells. Further, mice challenged with a GBSΔmprF mutant developed bacteremia comparably to wild-type (WT) infected mice yet had less recovered bacteria from brain tissue and a lower incidence of meningitis. Thus, our data suggest that Lys-Glc-DAG may contribute to bacterial uptake into host cells and disease progression. Importantly, our discovery provides a platform for further study of cationic lipids at the host–pathogen interface. Bacterial membrane lipids are critical for membrane bilayer formation, cell division, protein localization, stress responses, and pathogenesis. This study shows that the enzyme MprF in Streptococcus agalactiae synthesizes a novel cationic lipid, Lysyl-Glucosyl-Diacylglycerol, which aids meningitis progression in vivo.
Collapse
Affiliation(s)
- Luke R. Joyce
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Haider S. Manzer
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jéssica da C. Mendonça
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Rio de Janeiro State University, Roberto Alcântara Gomes Biology Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Villarreal
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Prescilla E. Nagao
- Rio de Janeiro State University, Roberto Alcântara Gomes Biology Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kelly S. Doran
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- * E-mail: (KSD); (KLP); (ZG)
| | - Kelli L. Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
- * E-mail: (KSD); (KLP); (ZG)
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (KSD); (KLP); (ZG)
| |
Collapse
|
10
|
Yakobov N, Mahmoudi N, Grob G, Yokokawa D, Saga Y, Kushiro T, Worrell D, Roy H, Schaller H, Senger B, Huck L, Riera Gascon G, Becker HD, Fischer F. RNA-dependent synthesis of ergosteryl-3β-O-glycine in Ascomycota expands the diversity of steryl-amino acids. J Biol Chem 2022; 298:101657. [PMID: 35131263 PMCID: PMC8913301 DOI: 10.1016/j.jbc.2022.101657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/11/2022] Open
|
11
|
York A, Lloyd AJ, Del Genio CI, Shearer J, Hinxman KJ, Fritz K, Fulop V, Dowson CG, Khalid S, Roper DI. Structure-based modeling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant present at the cytoplasmic membrane. Structure 2021; 29:731-742.e6. [PMID: 33740396 PMCID: PMC8280954 DOI: 10.1016/j.str.2021.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022]
Abstract
Branched Lipid II, required for the formation of indirectly crosslinked peptidoglycan, is generated by MurM, a protein essential for high-level penicillin resistance in the human pathogen Streptococcus pneumoniae. We have solved the X-ray crystal structure of Staphylococcus aureus FemX, an isofunctional homolog, and have used this as a template to generate a MurM homology model. Using this model, we perform molecular docking and molecular dynamics to examine the interaction of MurM with the phospholipid bilayer and the membrane-embedded Lipid II substrate. Our model suggests that MurM is associated with the major membrane phospholipid cardiolipin, and experimental evidence confirms that the activity of MurM is enhanced by this phospholipid and inhibited by its direct precursor phosphatidylglycerol. The spatial association of pneumococcal membrane phospholipids and their impact on MurM activity may therefore be critical to the final architecture of peptidoglycan and the expression of clinically relevant penicillin resistance in this pathogen.
Collapse
Affiliation(s)
- Anna York
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Adrian J Lloyd
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, University of Coventry, West Midlands CV1 5FB, UK
| | - Jonathan Shearer
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Karen J Hinxman
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Konstantin Fritz
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Vilmos Fulop
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Christopher G Dowson
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK.
| | - David I Roper
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK; Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
12
|
Phospholipid translocation captured in a bifunctional membrane protein MprF. Nat Commun 2021; 12:2927. [PMID: 34006869 PMCID: PMC8131360 DOI: 10.1038/s41467-021-23248-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/16/2021] [Indexed: 01/07/2023] Open
Abstract
As a large family of membrane proteins crucial for bacterial physiology and virulence, the Multiple Peptide Resistance Factors (MprFs) utilize two separate domains to synthesize and translocate aminoacyl phospholipids to the outer leaflets of bacterial membranes. The function of MprFs enables Staphylococcus aureus and other pathogenic bacteria to acquire resistance to daptomycin and cationic antimicrobial peptides. Here we present cryo-electron microscopy structures of MprF homodimer from Rhizobium tropici (RtMprF) at two different states in complex with lysyl-phosphatidylglycerol (LysPG). RtMprF contains a membrane-embedded lipid-flippase domain with two deep cavities opening toward the inner and outer leaflets of the membrane respectively. Intriguingly, a hook-shaped LysPG molecule is trapped inside the inner cavity with its head group bent toward the outer cavity which hosts a second phospholipid-binding site. Moreover, RtMprF exhibits multiple conformational states with the synthase domain adopting distinct positions relative to the flippase domain. Our results provide a detailed framework for understanding the mechanisms of MprF-mediated modification and translocation of phospholipids.
Collapse
|
13
|
Abstract
Bacteria are known to add amino acids (aa) to membrane lipids to resist antimicrobials and escape immune responses. This surface lipid aminoacylation process requires diverting aminoacyl-tRNAs from protein synthesis. While widespread in bacteria, no analogous lipid remodeling system had thus far been evidenced in eukaryotes. We uncovered that most fungi tRNA-dependently add aspartate onto ergosterol (ergosteryl-3β-O-l-aspartate [Erg-Asp]), the major sterol found in fungal membranes. Asp addition is catalyzed by an ergosteryl-3β-O-l-aspartate synthase (ErdS) and its removal by a dedicated hydrolase (ErdH). This pathway is conserved across “higher” fungi, including pathogens. Given the central roles of sterols and derivatives in fungi, we propose that the Erg-Asp homeostasis system might impact membrane remodeling, trafficking, antimicrobial resistance, or pathogenicity. Diverting aminoacyl-transfer RNAs (tRNAs) from protein synthesis is a well-known process used by a wide range of bacteria to aminoacylate membrane constituents. By tRNA-dependently adding amino acids to glycerolipids, bacteria change their cell surface properties, which intensifies antimicrobial drug resistance, pathogenicity, and virulence. No equivalent aminoacylated lipids have been uncovered in any eukaryotic species thus far, suggesting that tRNA-dependent lipid remodeling is a process restricted to prokaryotes. We report here the discovery of ergosteryl-3β-O-l-aspartate (Erg-Asp), a conjugated sterol that is produced by the tRNA-dependent addition of aspartate to the 3β-OH group of ergosterol, the major sterol found in fungal membranes. In fact, Erg-Asp exists in the majority of “higher” fungi, including species of biotechnological interest, and, more importantly, in human pathogens like Aspergillus fumigatus. We show that a bifunctional enzyme, ergosteryl-3β-O-l-aspartate synthase (ErdS), is responsible for Erg-Asp synthesis. ErdS corresponds to a unique fusion of an aspartyl-tRNA synthetase—that produces aspartyl-tRNAAsp (Asp-tRNAAsp)—and of a Domain of Unknown Function 2156, which actually transfers aspartate from Asp-tRNAAsp onto ergosterol. We also uncovered that removal of the Asp modifier from Erg-Asp is catalyzed by a second enzyme, ErdH, that is a genuine Erg-Asp hydrolase participating in the turnover of the conjugated sterol in vivo. Phylogenomics highlights that the entire Erg-Asp synthesis/degradation pathway is conserved across “higher” fungi. Given the central roles of sterols and conjugated sterols in fungi, we propose that this tRNA-dependent ergosterol modification and homeostasis system might have broader implications in membrane remodeling, trafficking, antimicrobial resistance, or pathogenicity.
Collapse
|
14
|
Abstract
The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Additionally, from the 22 proteinogenic aa, 13 are noncanonically used, by serving as substrates for the tRNA- or aa-tRNA-dependent synthesis of other cellular components. These nontranslational processes range from lipid aminoacylation, and heme, aa, antibiotic and peptidoglycan synthesis to protein degradation. This chapter focuses on these noncanonical usages of aa-tRNAs and the ways of generating them, and also highlights the strategies that cells have evolved to balance the use of aa-tRNAs between protein synthesis and synthesis of other cellular components.
Collapse
|
15
|
Small-Molecule Acetylation by GCN5-Related N-Acetyltransferases in Bacteria. Microbiol Mol Biol Rev 2020; 84:84/2/e00090-19. [PMID: 32295819 DOI: 10.1128/mmbr.00090-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Acetylation is a conserved modification used to regulate a variety of cellular pathways, such as gene expression, protein synthesis, detoxification, and virulence. Acetyltransferase enzymes transfer an acetyl moiety, usually from acetyl coenzyme A (AcCoA), onto a target substrate, thereby modulating activity or stability. Members of the GCN5- N -acetyltransferase (GNAT) protein superfamily are found in all domains of life and are characterized by a core structural domain architecture. These enzymes can modify primary amines of small molecules or of lysyl residues of proteins. From the initial discovery of antibiotic acetylation, GNATs have been shown to modify a myriad of small-molecule substrates, including tRNAs, polyamines, cell wall components, and other toxins. This review focuses on the literature on small-molecule substrates of GNATs in bacteria, including structural examples, to understand ligand binding and catalysis. Understanding the plethora and versatility of substrates helps frame the role of acetylation within the larger context of bacterial cellular physiology.
Collapse
|
16
|
Wang SC, Davejan P, Hendargo KJ, Javadi-Razaz I, Chou A, Yee DC, Ghazi F, Lam KJK, Conn AM, Madrigal A, Medrano-Soto A, Saier MH. Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183277. [PMID: 32205149 DOI: 10.1016/j.bbamem.2020.183277] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/14/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022]
Abstract
The Major Facilitator Superfamily (MFS) is currently the largest characterized superfamily of transmembrane secondary transport proteins. Its diverse members are found in essentially all organisms in the biosphere and function by uniport, symport, and/or antiport mechanisms. In 1993 we first named and described the MFS which then consisted of 5 previously known families that had not been known to be related, and by 2012 we had identified a total of 74 families, classified phylogenetically within the MFS, all of which included only transport proteins. This superfamily has since expanded to 89 families, all included under TC# 2.A.1, and a few transporter families outside of TC# 2.A.1 were identified as members of the MFS. In this study, we assign nine previously unclassified protein families in the Transporter Classification Database (TCDB; http://www.tcdb.org) to the MFS based on multiple criteria and bioinformatic methodologies. In addition, we find integral membrane domains distantly related to partial or full-length MFS permeases in Lysyl tRNA Synthases (TC# 9.B.111), Lysylphosphatidyl Glycerol Synthases (TC# 4.H.1), and cytochrome b561 transmembrane electron carriers (TC# 5.B.2). Sequence alignments, overlap of hydropathy plots, compatibility of repeat units, similarity of complexity profiles of transmembrane segments, shared protein domains and 3D structural similarities between transport proteins were analyzed to assist in inferring homology. The MFS now includes 105 families.
Collapse
Affiliation(s)
- Steven C Wang
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Pauldeen Davejan
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Kevin J Hendargo
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Ida Javadi-Razaz
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Amy Chou
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Daniel C Yee
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Faezeh Ghazi
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Katie Jing Kay Lam
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Adam M Conn
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Assael Madrigal
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Arturo Medrano-Soto
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America
| | - Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, United States of America.
| |
Collapse
|
17
|
Mendoza-Macías CL, Solorio-Alvarado CR, Alonso-Castro AJ, Alba-Betancourt C, Deveze-Álvarez MA, Padilla-Vaca F, Reyes-Gualito A. Discovery of new effective N-alkyl-3,4-diarylmaleimides-based drugs for reversing the bacterial resistance to rhodamine 6G in Bacillus subtilis. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00992-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
18
|
Mechanism of regulation and neutralization of the AtaR–AtaT toxin–antitoxin system. Nat Chem Biol 2019; 15:285-294. [DOI: 10.1038/s41589-018-0216-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/14/2018] [Indexed: 11/08/2022]
|
19
|
Kumariya R, Garsa AK, Rajput YS, Sood SK, Akhtar N, Patel S. Bacteriocins: Classification, synthesis, mechanism of action and resistance development in food spoilage causing bacteria. Microb Pathog 2019; 128:171-177. [PMID: 30610901 DOI: 10.1016/j.micpath.2019.01.002] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 01/06/2023]
Abstract
Huge demand of safe and natural preservatives has opened new area for intensive research on bacteriocins to unravel the novel range of antimicrobial compounds that could efficiently fight off the food-borne pathogens. Since food safety has become an increasingly important international concern, the application of bacteriocins from lactic acid bacteria that target food spoilage/pathogenic bacteria without major adverse effects has received great attention. Different modes of actions of these bacteriocins have been suggested and identified, like pore-forming, inhibition of cell-wall/nucleic acid/protein synthesis. However, development of resistance in the food spoilage and pathogenic bacteria against these bacteriocins is a rising concern. Emergence and spread of mutant strains resistant to bacteriocins is hampering food safety. It has spurred an interest to understand the bacteriocin resistance phenomenon displayed by the food pathogens, which will be helpful in mitigating the resistance problem. Therefore, present review is focused on the different resistance mechanisms adopted by food pathogens to overcome bacteriocin.
Collapse
Affiliation(s)
- Rashmi Kumariya
- Protein Expression and Purification Facility, Advanced Technology Platform Centre, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India.
| | - Anita Kumari Garsa
- Division of Dairy Microbiology, National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Y S Rajput
- Division of Animal Biochemistry, National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - S K Sood
- Division of Animal Biochemistry, National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Nadeem Akhtar
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, 92182, USA
| |
Collapse
|
20
|
Groenewold MK, Hebecker S, Fritz C, Czolkoss S, Wiesselmann M, Heinz DW, Jahn D, Narberhaus F, Aktas M, Moser J. Virulence of Agrobacterium tumefaciens requires lipid homeostasis mediated by the lysyl-phosphatidylglycerol hydrolase AcvB. Mol Microbiol 2018; 111:269-286. [PMID: 30353924 DOI: 10.1111/mmi.14154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2018] [Indexed: 12/24/2022]
Abstract
Agrobacterium tumefaciens transfers oncogenic T-DNA via the type IV secretion system (T4SS) into plants causing tumor formation. The acvB gene encodes a virulence factor of unknown function required for plant transformation. Here we specify AcvB as a periplasmic lysyl-phosphatidylglycerol (L-PG) hydrolase, which modulates L-PG homeostasis. Through functional characterization of recombinant AcvB variants, we showed that the C-terminal domain of AcvB (residues 232-456) is sufficient for full enzymatic activity and defined key residues for catalysis. Absence of the hydrolase resulted in ~10-fold increase in L-PG in Agrobacterium membranes and abolished T-DNA transfer and tumor formation. Overproduction of the L-PG synthase gene (lpiA) in wild-type A. tumefaciens resulted in a similar increase in the L-PG content (~7-fold) and a virulence defect even in the presence of intact AcvB. These results suggest that elevated L-PG amounts (either by overproduction of the synthase or absence of the hydrolase) are responsible for the virulence phenotype. Gradually increasing the L-PG content by complementation with different acvB variants revealed that cellular L-PG levels above 3% of total phospholipids interfere with T-DNA transfer. Cumulatively, this study identified AcvB as a novel virulence factor required for membrane lipid homeostasis and T-DNA transfer.
Collapse
Affiliation(s)
- Maike K Groenewold
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Stefanie Hebecker
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Christiane Fritz
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Simon Czolkoss
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Milan Wiesselmann
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Dirk W Heinz
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Dieter Jahn
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Franz Narberhaus
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Meriyem Aktas
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Jürgen Moser
- Institute for Microbiology, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| |
Collapse
|
21
|
Ulrich EC, Bougioukou DJ, van der Donk WA. Investigation of Amide Bond Formation during Dehydrophos Biosynthesis. ACS Chem Biol 2018; 13:537-541. [PMID: 29303545 DOI: 10.1021/acschembio.7b00949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehydrophos is a tripeptide phosphonate antibiotic produced by Streptomyces luridus. Its biosynthetic pathway involves the use of aminoacyl-tRNA (aa-tRNA) for amide bond formation. The first amide bond during biosynthesis is formed by DhpH-C, a peptidyltransferase that utilizes Leu-tRNALeu. DhpH-C is a member of a burgeoning family of natural product biosynthetic enzymes that make use of aa-tRNA outside of canonical translation activities in the cell. Here, we used site-directed mutagenesis of both DhpH-C and tRNALeu to investigate the enzyme mechanism and substrate specificity, respectively, and analyzed the substrate scope for the production of a set of dipeptides. DhpH-C appears to recognize both the amino acyl group on the tRNA and the tRNA acceptor stem, and the enzyme can accept other hydrophobic residues, in addition to leucine. These results contribute to a better understanding of enzyme-aa-tRNA interactions and the growing exploration of aa-tRNA usage beyond translation.
Collapse
|
22
|
Luo Y, Javed MA, Deneer H. Comparative study on nutrient depletion-induced lipidome adaptations in Staphylococcus haemolyticus and Staphylococcus epidermidis. Sci Rep 2018; 8:2356. [PMID: 29402937 PMCID: PMC5799182 DOI: 10.1038/s41598-018-20801-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/24/2018] [Indexed: 11/09/2022] Open
Abstract
Staphylococcus species are emerging opportunistic pathogens that cause outbreaks of hospital and community-acquired infections. Some of these bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) are difficult to treat due to their resistance to multiple antibiotics. We carried out a comparative study on the lipidome adaptations in response to starvation in the two most common coagulase-negative Staphylococcus species: a S. epidermidis strain sensitive to ampicillin and erythromycin and a S. haemolyticus strain resistant to both. The predominant fatty acid composition in glycerolipids was (17:0-15:0) in both bacteria. During the exponential phase, the two bacterial lipidomes were similar. Both were dominated by diacylglycerol (DAG), phosphatidylglycerol (PG), lysyl-phosphatidylglycerol (Lysyl-PG) and Diglucosyl-diacylglycerol (DGDG). Alanyl-PG was detected in small amounts in both bacterial lipids. N-succinyl-lysyl-PG was detected only in S. haemolyticus, while lysyl-DAG only in S. epidermidis. As the two bacteria entered stationary phase, both lipidomes became essentially nitrogen-free. Both bacteria accumulated large amounts of free fatty acids. Strikingly, the lipidome of S. epidermidis became dominated by cardiolipin (CL), while that of S. haemolyticus was simplified to DGDG and PG. The S. epidermidis strain also produced acyl-phosphatidylglycerol (APG) in the stationary phase.
Collapse
Affiliation(s)
- Yu Luo
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| | - Muhammad Afzal Javed
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Harry Deneer
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Molecular Microbiology Laboratory, Division of Clinical Microbiology, Saskatoon Health Region, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
23
|
Fields RN, Roy H. Deciphering the tRNA-dependent lipid aminoacylation systems in bacteria: Novel components and structural advances. RNA Biol 2017; 15:480-491. [PMID: 28816600 PMCID: PMC6103681 DOI: 10.1080/15476286.2017.1356980] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
tRNA-dependent addition of amino acids to lipids on the outer surface of the bacterial membrane results in decreased effectiveness of antimicrobials such as cationic antimicrobial peptides (CAMPs) that target the membrane, and increased virulence of several pathogenic species. After a brief introduction to CAMPs and the various bacterial resistance mechanisms used to counteract these compounds, this review focuses on recent advances in tRNA-dependent pathways for lipid modification in bacteria. Phenotypes associated with amino acid lipid modifications and regulation of their expression will also be discussed.
Collapse
Affiliation(s)
- Rachel N Fields
- a Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando , Florida , United States of America
| | - Hervé Roy
- a Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida , Orlando , Florida , United States of America
| |
Collapse
|
24
|
Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| |
Collapse
|
25
|
Moutiez M, Belin P, Gondry M. Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. Chem Rev 2017; 117:5578-5618. [DOI: 10.1021/acs.chemrev.6b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mireille Moutiez
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Pascal Belin
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| |
Collapse
|
26
|
Slavetinsky C, Kuhn S, Peschel A. Bacterial aminoacyl phospholipids - Biosynthesis and role in basic cellular processes and pathogenicity. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1310-1318. [PMID: 27940309 DOI: 10.1016/j.bbalip.2016.11.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 10/20/2022]
Abstract
The bacterial cell membrane accomplishes the controlled exchange of molecules with the extracellular space and mediates specific interactions with the environment. However, the cytoplasmic membrane also includes vulnerable targets for antimicrobial agents. A common feature of cationic antimicrobial peptides (CAMPs) produced by other bacteria or by the host immune system is to utilize the negative charge of bacterial phospholipids such as phosphatidylglycerol (PG) or cardiolipin (CL) for initial adherence and subsequent penetration into the membrane bilayer. To resist cationic antimicrobials many bacteria integrate positive charges into the membrane surface. This is accomplished by aminoacylation of negatively charged (PG) or (CL) with alanine, arginine, or lysine residues. The Multiple Peptide Resistance Factor (MprF) of Staphylococcus aureus is the prototype of a highly conserved protein family of aminoacyl phosphatidylglycerol synthases (aaPGSs) which modify PG or CL with amino acids. MprF is an oligomerizing membrane protein responsible for both, synthesis of lysyl phosphatidylglycerol (LysPG) in the inner leaflet of the cytoplasmic membrane and translocation of LysPG to the outer leaflet. This review focuses on occurrence, synthesis and function of bacterial aminoacyl phospholipids (aaPLs) and on the role of such lipids in basic cellular processes and pathogenicity. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
Collapse
Affiliation(s)
- Christoph Slavetinsky
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Sebastian Kuhn
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, 72076 Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany.
| |
Collapse
|
27
|
Ulrich EC, van der Donk WA. Cameo appearances of aminoacyl-tRNA in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:29-36. [PMID: 27599269 PMCID: PMC5161580 DOI: 10.1016/j.cbpa.2016.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/22/2016] [Indexed: 11/19/2022]
Abstract
The breadth of unprecedented enzymatic reactions performed during the formation of microbial natural products has continued to expand as new biosynthetic gene clusters are unearthed by genome mining. Enzymes that use aminoacyl-tRNA (aa-tRNA) outside of the translation machinery have been known for decades, and accounts of their use in natural product biosynthesis are just beginning to accumulate. This review will highlight the recent discoveries and advances in our mechanistic understanding of aa-tRNA-dependent enzymes that play key roles in the biosynthesis of a growing number of microbial natural products.
Collapse
Affiliation(s)
- Emily C Ulrich
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA.
| |
Collapse
|
28
|
Atila M, Katselis G, Chumala P, Luo Y. Characterization of N-Succinylation of L-Lysylphosphatidylglycerol in Bacillus subtilis Using Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1606-1613. [PMID: 27506207 DOI: 10.1007/s13361-016-1455-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 06/06/2023]
Abstract
Phospholipids generally dominate in bacterial lipids. The negatively charged nature of phospholipids renders bacteria susceptible to cationic antibiotic peptides. In comparison with Gram-negative bacteria, Gram-positive bacteria in general have much less zwitterionic phosphatidylethanolamine. However, they are known for producing aminoacylated phosphatidylglycerol (PG), especially positively charged L-lysyl-PG, which is catalyzed by lysyl-PG synthase MprF, which appears to have a broad range of specificity for L-aminoacyl transfer RNAs. In addition, many Gram-positive bacteria also have a dlt-gene-coded D-alanylation pathway for lipoteichoic acids and wall teichoic acids covalently attached to a glycolipid or peptidoglycan. D-Alanylation also masks the dominant negative charge of the phosphate-rich polymers of teichoic acids. Using mass spectrometry, we have recently observed that precursor scans in negative mode for deprotonated amino acid fragments were most sensitive for ester-linked amino acids. Such a scan for precursors generating an m/z 145 lysyl anion revealed lysyl-PG as well as an additional species 100 m/z units greater than lysyl-PG. This unexpected species corresponded precisely to the expected mass of N-succinylated lysyl-PG. Tandem mass spectrometry revealed a precise match to the fragmentation pattern of this putative new species. PG, lysyl-PG, and N-succinyl-lysyl-PG may form a complete loop of charge reversal from -1 to +1 and then back to -1. Analogous charge reversal by N-succinylation of lysine residues in the bacterial as well as eukaryotic proteomes has been recently discovered as a major posttranslational modification. Such modification in bacterial lipids is possibly catalyzed by an enzyme homologous to the enzymes that modify lysine residues in proteins. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Metin Atila
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - George Katselis
- Canadian Centre for Health and Safety in Agriculture/Department of Medicine, Core Mass Spectrometry Facility, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Paulos Chumala
- Canadian Centre for Health and Safety in Agriculture/Department of Medicine, Core Mass Spectrometry Facility, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yu Luo
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| |
Collapse
|
29
|
Pomorski TG, Menon AK. Lipid somersaults: Uncovering the mechanisms of protein-mediated lipid flipping. Prog Lipid Res 2016; 64:69-84. [PMID: 27528189 DOI: 10.1016/j.plipres.2016.08.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/10/2016] [Indexed: 12/22/2022]
Abstract
Membrane lipids diffuse rapidly in the plane of the membrane but their ability to flip spontaneously across a membrane bilayer is hampered by a significant energy barrier. Thus spontaneous flip-flop of polar lipids across membranes is very slow, even though it must occur rapidly to support diverse aspects of cellular life. Here we discuss the mechanisms by which rapid flip-flop occurs, and what role lipid flipping plays in membrane homeostasis and cell growth. We focus on conceptual aspects, highlighting mechanistic insights from biochemical and in silico experiments, and the recent, ground-breaking identification of a number of lipid scramblases.
Collapse
Affiliation(s)
- Thomas Günther Pomorski
- Faculty of Chemistry and Biochemistry, Molecular Biochemistry, Ruhr University Bochum, Universitätstrasse 150, D-44780 Bochum, Germany; Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
30
|
tRNA-Dependent Aminoacylation of an Amino Sugar Intermediate in the Biosynthesis of a Streptothricin-Related Antibiotic. Appl Environ Microbiol 2016; 82:3640-8. [PMID: 27084005 DOI: 10.1128/aem.00725-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/07/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The antibiotic streptothricin (ST) possesses an amino sugar bound to an l-β-lysine (β-Lys) residue via a peptide bond. The peptide bond formation has been shown to be catalyzed by a nonribosomal peptide synthetase (NRPS) during ST biosynthesis. The focus of this study is the closely related ST analogue BD-12, which carries a glycine-derived side chain rather than a β-Lys residue. Here, in Streptomyces luteocolor NBRC13826, we describe our biosynthetic studies of BD-12, which revealed that the peptide bond between the amino sugar and the glycine residue is catalyzed by a Fem-like enzyme (Orf11) in a tRNA-dependent manner rather than by an NRPS. Although there have been several reports of peptide bond-forming tRNA-dependent enzymes, to our knowledge, Orf11 is the first enzyme that can accept an amino sugar as a substrate. Our findings clearly demonstrate that the structural diversity of the side chains of ST-type compounds in nature is generated in an unusual manner via two distinct peptide bond-forming mechanisms. Moreover, the identification and functional analysis of Orf11 resulted in not only the production of new ST-related compounds, but also the provision of new insights into the structure-activity relationship of the ST-related antibiotics. IMPORTANCE The antibiotic streptothricin (ST) possesses an amino sugar bound to an l-β-lysine (β-Lys) side chain via a peptide bond formed by a nonribosomal peptide synthetase (NRPS). BD-12, an analogue of ST, carries a glycine-derived side chain rather than β-Lys, and here, we describe the BD-12-biosynthetic gene cluster from Streptomyces luteocolor NBRC13826, which contains the orf11 gene encoding a novel tRNA-dependent peptide bond-forming enzyme. The unique Fem-like enzyme (Orf11) accepts the amino sugar as a substrate and mediates the peptide formation between the amino sugar intermediate and glycine. Our studies demonstrate that the structural diversity of the side chains of ST-related compounds in nature is generated via two distinct peptide bond-forming mechanisms.
Collapse
|
31
|
Atila M, Luo Y. Profiling and tandem mass spectrometry analysis of aminoacylated phospholipids in Bacillus subtilis . F1000Res 2016; 5:121. [PMID: 26998233 PMCID: PMC4792211 DOI: 10.12688/f1000research.7842.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2016] [Indexed: 01/13/2023] Open
Abstract
Cationic modulation of the dominantly negative electrostatic structure of phospholipids plays an important role in bacterial response to changes in the environment. In addition to zwitterionic phosphatidylethanolamine, Gram-positive bacteria are also abundant in positively charged lysyl-phosphatidylglycerol. Increased amounts of both types of lipids render Gram-positive bacterial cells more resistant to cationic antibiotic peptides such as defensins. Lysyl and alanyl-phosphatidylglycerol as well as alanyl-cardiolipin have also been studied by mass spectroscopy. Phospholipids modified by other amino acids have been discovered by chemical analysis of the lipid lysate but have yet to be studied by mass spectroscopy. We exploited the high sensitivity of modern mass spectroscopy in searching for substructures in complex mixtures to establish a sensitive and thorough screen for aminoacylated phospholipids. The search for deprotonated aminoacyl anions in lipid extracted from
Bacillus subtilis strain 168 yielded strong evidence as well as relative abundance of aminoacyl-phosphatidylglycerols, which serves as a crude measure of the specificity of aminoacyl-phosphatidylglycerol synthase MprF. No aminoacyl-cardiolipin was found. More importantly, the second most abundant species in this category is D-alanyl-phosphatidylglycerol, suggesting a possible role in the D-alanylation pathway of wall- and lipo-teichoic acids.
Collapse
Affiliation(s)
- Metin Atila
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| |
Collapse
|
32
|
Fung AWS, Payoe R, Fahlman RP. Perspectives and Insights into the Competition for Aminoacyl-tRNAs between the Translational Machinery and for tRNA Dependent Non-Ribosomal Peptide Bond Formation. Life (Basel) 2015; 6:life6010002. [PMID: 26729173 PMCID: PMC4810233 DOI: 10.3390/life6010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/23/2015] [Accepted: 12/25/2015] [Indexed: 12/19/2022] Open
Abstract
Aminoacyl-tRNA protein transferases catalyze the transfer of amino acids from aminoacyl-tRNAs to polypeptide substrates. Different forms of these enzymes are found in the different kingdoms of life and have been identified to be central to a wide variety of cellular processes. L/F-transferase is the sole member of this class of enzyme found in Escherichia coli and catalyzes the transfer of leucine to the N-termini of proteins which result in the targeted degradation of the modified protein. Recent investigations on the tRNA specificity of L/F-transferase have revealed the unique recognition nucleotides for a preferred Leu-tRNALeu isoacceptor substrate. In addition to discussing this tRNA selectivity by L/F-transferase, we present and discuss a hypothesis and its implications regarding the apparent competition for this aminoacyl-tRNA between L/F-transferase and the translational machinery. Our discussion reveals a hypothetical involvement of the bacterial stringent response that occurs upon amino acid limitation as a potential cellular event that may reduce this competition and provide the opportunity for L/F-transferase to readily increase its access to the pool of aminoacylated tRNA substrates.
Collapse
Affiliation(s)
- Angela W S Fung
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada.
| | - Roshani Payoe
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Institute of Technology, Faculty of Science and Technology, University of Tartu, Noorse St 1, Tartu 50411, Estonia.
| | - Richard P Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| |
Collapse
|