1
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Beliakoff RE, Gonzalez CF, Lorca GL. Bile promotes Lactobacillus johnsonii N6.2 extracellular vesicle production with conserved immunomodulatory properties. Sci Rep 2024; 14:12272. [PMID: 38806562 PMCID: PMC11133329 DOI: 10.1038/s41598-024-62843-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
Recently, Lactobacillus johnsonii N6.2-derived extracellular vesicles (EVs) were shown to reduce apoptosis in human beta cell lines and stimulate insulin secretion in human islets. Our goal was to identify a physiologically relevant environmental condition that induces a hypervesiculation phenotype in L. johnsonii N6.2 and to evaluate if transcriptional changes are involved in this process. Culturing this strain in the presence of 0.2% bovine bile, which mimics a stressor encountered by the bacterium in the small intestine, resulted in approximately a 100-fold increase in EVs relative to cells grown in media without bile. Whole transcriptome analysis of cells grown with bile revealed upregulation of several peptidoglycan hydrolases as well as several genes involved in fatty acid utilization. These results suggest that the hypervesiculation phenotype may be the result of increased cell wall turnover combined with increased accumulation of phospholipids, in agreement with our previous proteomic and lipidomics results. Additionally, EVs isolated from L. johnsonii N6.2 grown in presence of bile maintained their immunomodulatory properties in host-derived βlox5 pancreatic and THP-1 macrophage cell lines. Our findings suggest that in L. johnsonii N6.2 vesiculogenesis is significantly impacted by the expression of cell wall modifying enzymes and proteins utilized for exogenous fatty acid uptake that are regulated at the transcriptional level. Furthermore, this data suggests that vesiculogenesis could be stimulated in vivo using small molecules thereby maximizing the beneficial interactions between bacteria and their hosts.
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Affiliation(s)
- Reagan E Beliakoff
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Claudio F Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Graciela L Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
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2
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Chen H, Shi Y, Huang M, Lu T, Zhang H, Zhou C, Hou T, Feng Y. Recognition and acquisition of FakB2-loaded exogenous fatty acid (eFA) by a streptococcal FakA kinase. Sci Bull (Beijing) 2024:S2095-9273(24)00349-9. [PMID: 38806393 DOI: 10.1016/j.scib.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/12/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Affiliation(s)
- Haiyi Chen
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Shi
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Man Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ting Lu
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana 61801, USA
| | - Huimin Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana 61801, USA
| | - Chun Zhou
- School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Youjun Feng
- Key Laboratory of Multiple Organ Failure, Ministry of Education, Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Clinical Laboratory, Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518444, China.
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3
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Zou Q, Dong H, Cronan JE. Growth of Enterococcus faecalis ∆ plsX strains is restored by increased saturated fatty acid synthesis. mSphere 2023; 8:e0012023. [PMID: 37289195 PMCID: PMC10449490 DOI: 10.1128/msphere.00120-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/07/2023] [Indexed: 06/09/2023] Open
Abstract
The Enterococcus faecalis acyl-acyl carrier protein (ACP) phosphate acyltransferase PlsX plays an important role in phospholipid synthesis and exogenous fatty acid incorporation. Loss of plsX almost completely blocks growth by decreasing de novo phospholipid synthesis, which leads to abnormally long-chain acyl chains in the cell membrane phospholipids. The ∆plsX strain failed to grow without supplementation with an appropriate exogenous fatty acid. Introduction of a ∆fabT mutation into the ∆plsX strain to increase fatty acid synthesis allowed very weak growth. The ∆plsX strain accumulated suppressor mutants. One of these encoded a truncated β-ketoacyl-ACP synthase II (FabO) which restored normal growth and restored de novo phospholipid acyl chain synthesis by increasing saturated acyl-ACP synthesis. Saturated acyl-ACPs are cleaved by a thioesterase to provide free fatty acids for conversion to acyl-phosphates by the FakAB system. The acyl-phosphates are incorporated into position sn1 of the phospholipids by PlsY. We report the tesE gene encodes a thioesterase that can provide free fatty acids. However, we were unable to delete the chromosomal tesE gene to confirm that it is the responsible enzyme. TesE readily cleaves unsaturated acyl-ACPs, whereas saturated acyl-ACPs are cleaved much more slowly. Overexpression of an E. faecalis enoyl-ACP reductase either FabK or FabI which results in high levels of saturated fatty acid synthesis also restored the growth of the ∆plsX strain. The ∆plsX strain grew faster in the presence of palmitic acid than in the presence of oleic acid with improvement in phospholipid acyl chain synthesis. Positional analysis of the acyl chain distribution in the phospholipids showed that saturated acyl chains dominate the sn1-position indicating a preference for saturated fatty acids at this position. High-level production of saturated acyl-ACPs is required to offset the marked preference of the TesE thioesterase for unsaturated acyl-ACPs and allow the initiation of phospholipid synthesis.
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Affiliation(s)
- Qi Zou
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Huijuan Dong
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John E. Cronan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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4
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Wei Y, Sturges CI, Palmer KL. Human Serum Supplementation Promotes Streptococcus mitis Growth and Induces Specific Transcriptomic Responses. Microbiol Spectr 2023; 11:e0512922. [PMID: 37014220 PMCID: PMC10269507 DOI: 10.1128/spectrum.05129-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/01/2023] [Indexed: 04/05/2023] Open
Abstract
Streptococcus mitis is a normal member of the human oral microbiota and a leading opportunistic pathogen causing infective endocarditis (IE). Despite the complex interactions between S. mitis and the human host, understanding of S. mitis physiology and its mechanisms of adaptation to host-associated environments is inadequate, especially compared with other IE bacterial pathogens. This study reports the growth-promoting effects of human serum on S. mitis and other pathogenic streptococci, including S. oralis, S. pneumoniae, and S. agalactiae. Using transcriptomic analyses, we identified that, with the addition of human serum, S. mitis downregulates uptake systems for metal ions and sugars, fatty acid biosynthetic genes, and genes involved in stress response and other processes related with growth and replication. S. mitis upregulates uptake systems for amino acids and short peptides in response to human serum. Zinc availability and environmental signals sensed by the induced short peptide binding proteins were not sufficient to confer the growth-promoting effects. More investigation is required to establish the mechanism for growth promotion. Overall, our study contributes to the fundamental understanding of S. mitis physiology under host-associated conditions. IMPORTANCE S. mitis is exposed to human serum components during commensalism in the human mouth and bloodstream pathogenesis. However, the physiological effects of serum components on this bacterium remain unclear. Using transcriptomic analyses, S. mitis biological processes that respond to the presence of human serum were revealed, improving the fundamental understanding of S. mitis physiology in human host conditions.
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Affiliation(s)
- Yahan Wei
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Camille I. Sturges
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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5
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Radka CD. Interfacial Enzymes Enable Gram-Positive Microbes to Eat Fatty Acids. MEMBRANES 2023; 13:423. [PMID: 37103850 PMCID: PMC10146087 DOI: 10.3390/membranes13040423] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 06/19/2023]
Abstract
Exogenous fatty acid (eFA) activation and utilization play key roles in bacterial physiology and confer growth advantages by bypassing the need to make fatty acids for lipid synthesis. In Gram-positive bacteria, eFA activation and utilization is generally carried out by the fatty acid kinase (FakAB) two-component system that converts eFA to acyl phosphate, and the acyl-ACP:phosphate transacylase (PlsX) that catalyzes the reversible conversion of acyl phosphate to acyl-acyl carrier protein. Acyl-acyl carrier protein is a soluble format of the fatty acid that is compatible with cellular metabolic enzymes and can feed multiple processes including the fatty acid biosynthesis pathway. The combination of FakAB and PlsX enables the bacteria to channel eFA nutrients. These key enzymes are peripheral membrane interfacial proteins that associate with the membrane through amphipathic helices and hydrophobic loops. In this review, we discuss the biochemical and biophysical advances that have established the structural features that drive FakB or PlsX association with the membrane, and how these protein-lipid interactions contribute to enzyme catalysis.
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Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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6
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Pettersen JS, Høg FF, Nielsen FD, Møller-Jensen J, Jørgensen MG. Global transcriptional responses of pneumococcus to human blood components and cerebrospinal fluid. Front Microbiol 2022; 13:1060583. [PMID: 36620004 PMCID: PMC9812572 DOI: 10.3389/fmicb.2022.1060583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a leading cause of severe invasive infectious diseases such as sepsis and meningitis. Understanding how pneumococcus adapts and survive in the human bloodstream environment and cerebrospinal fluid (CSF) is important for development of future treatment strategies. This study investigates the global transcriptional response of pneumococcus to human blood components and CSF acquired from discarded and anonymized patient samples. Extensive transcriptional changes to human blood components were observed during early stages of interaction. Plasma-specific responses were primarily related to metabolic components and include strong downregulation of fatty acid biosynthesis genes, and upregulation of nucleotide biosynthesis genes. No transcriptional responses specific to the active plasma proteins (e.g., complement proteins) were observed during early stages of interaction as demonstrated by a differential expression analysis between plasma and heat-inactivated plasma. The red blood cell (RBC)-specific response was far more complex, and included activation of the competence system, differential expression of several two-component systems, phosphotransferase systems and transition metal transporter genes. Interestingly, most of the changes observed for CSF were also observed for plasma. One of the few CSF-specific responses, not observed for plasma, was a strong downregulation of the iron acquisition system piuBCDA. Intriguingly, this transcriptomic analysis also uncovers significant differential expression of more than 20 small non-coding RNAs, most of them in response to RBCs, including small RNAs from uncharacterized type I toxin-antitoxin systems. In summary, this transcriptomic study identifies key pneumococcal metabolic pathways and regulatory genes involved with adaptation to human blood and CSF. Future studies should uncover the potential involvement of these factors with virulence in-vivo.
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7
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Nakatani M, Nakahara SY, Fukui K, Urano M, Fujii Y, Murakawa T, Baba S, Kumasaka T, Okanishi H, Kanai Y, Yano T, Masui R. Crystal structure of a nucleotide-binding domain of fatty acid kinase FakA from Thermus thermophilus HB8. J Struct Biol 2022; 214:107904. [PMID: 36228973 DOI: 10.1016/j.jsb.2022.107904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 12/04/2022]
Abstract
Fatty acid kinase is necessary for the incorporation of exogenous fatty acids into membrane phospholipids. Fatty acid kinase consists of two components: a kinase component, FakA, that phosphorylates a fatty acid bound to a fatty acid-binding component, FakB. However, the molecular details underlying the phosphotransfer reaction remain to be resolved. We determined the crystal structure of the N-terminal domain of FakA bound to ADP from Thermus thermophilus HB8. The overall structure of this domain showed that the helical barrel fold is similar to the nucleotide-binding component of dihydroxyacetone kinase. The structure of the nucleotide-binding site revealed the roles of the conserved residues in recognition of ADP and Mg2+, but the N-terminal domain of FakA lacked the ADP-capping loop found in the dihydroxyacetone kinase component. Based on the structural similarity to the two subunits of dihydroxyacetone kinase complex, we constructed a model of the complex of T. thermophilus FakB and the N-terminal domain of FakA. In this model, the invariant Arg residue of FakB occupied a position that was spatially similar to that of the catalytically important Arg residue of dihydroxyacetone kinase, which predicted a composite active site in the Fatty acid kinase complex.
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Affiliation(s)
- Maya Nakatani
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Shun-Ya Nakahara
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Kenji Fukui
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Momoka Urano
- Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yuki Fujii
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Seiki Baba
- The Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- The Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Hyogo 679-5198, Japan
| | - Hiroki Okanishi
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Yoshikatsu Kanai
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Ryoji Masui
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan; Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.
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8
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Shi Y, Zang N, Lou N, Xu Y, Sun J, Huang M, Zhang H, Lu H, Zhou C, Feng Y. Structure and mechanism for streptococcal fatty acid kinase (Fak) system dedicated to host fatty acid scavenging. SCIENCE ADVANCES 2022; 8:eabq3944. [PMID: 36054360 PMCID: PMC10848957 DOI: 10.1126/sciadv.abq3944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Staphylococcus and Streptococcus, two groups of major human pathogens, are equipped with a fatty acid kinase (Fak) machinery to scavenge host fatty acids. The Fak complex is contains an ATP-binding subunit FakA, which interacts with varied FakB isoforms, and synthesizes acyl-phosphate from extracellular fatty acids. However, how FakA recognizes its FakB partners and then activates different fatty acids is poorly understood. Here, we systematically describe the Fak system from the zoonotic pathogen, Streptococcus suis. The crystal structure of SsFakA complexed with SsFakB2 was determined at 2.6 Å resolution. An in vitro system of Fak-PlsX (phosphate: acyl-ACP transacylase) was developed to track acyl-phosphate intermediate and its final product acyl-ACP. Structure-guided mutagenesis enabled us to characterize a mechanism for streptococcal FakA working with FakB partners engaged in host fatty acid scavenging. These findings offer a comprehensive description of the Fak kinase machinery, thus advancing the discovery of attractive targets against deadly infections with Streptococcus.
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Affiliation(s)
- Yu Shi
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Ning Zang
- Department of Toxicology, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Ningjie Lou
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yongchang Xu
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingdu Sun
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Man Huang
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Huimin Zhang
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chun Zhou
- Department of Toxicology, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Youjun Feng
- Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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9
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Raita Y, Pérez-Losada M, Freishtat RJ, Hahn A, Castro-Nallar E, Ramos-Tapia I, Stearrett N, Bochkov YA, Gern JE, Mansbach JM, Zhu Z, Camargo CA, Hasegawa K. Nasopharyngeal metatranscriptome profiles of infants with bronchiolitis and risk of childhood asthma: a multicentre prospective study. Eur Respir J 2022; 60:2102293. [PMID: 34916264 PMCID: PMC9206513 DOI: 10.1183/13993003.02293-2021] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/17/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Bronchiolitis is not only the leading cause of hospitalisation in US infants but also a major risk factor for asthma development. Growing evidence supports clinical heterogeneity within bronchiolitis. Our objectives were to identify metatranscriptome profiles of infant bronchiolitis, and to examine their relationship with the host transcriptome and subsequent asthma development. METHODS As part of a multicentre prospective cohort study of infants (age <1 year) hospitalised for bronchiolitis, we integrated virus and nasopharyngeal metatranscriptome (species-level taxonomy and function) data measured at hospitalisation. We applied network-based clustering approaches to identify metatranscriptome profiles. We then examined their association with the host transcriptome at hospitalisation and risk for developing asthma. RESULTS We identified five metatranscriptome profiles of bronchiolitis (n=244): profile A: virusRSVmicrobiomecommensals; profile B: virusRSV/RV-Amicrobiome H.influenzae ; profile C: virusRSVmicrobiome S.pneumoniae ; profile D: virusRSVmicrobiome M.nonliquefaciens ; and profile E: virusRSV/RV-Cmicrobiome M.catarrhalis . Compared with profile A, profile B infants were characterised by a high proportion of eczema, Haemophilus influenzae abundance and enriched virulence related to antibiotic resistance. These profile B infants also had upregulated T-helper 17 and downregulated type I interferon pathways (false discovery rate (FDR) <0.005), and significantly higher risk for developing asthma (17.9% versus 38.9%; adjusted OR 2.81, 95% CI 1.11-7.26). Likewise, profile C infants were characterised by a high proportion of parental asthma, Streptococcus pneumoniae dominance, and enriched glycerolipid and glycerophospholipid metabolism of the microbiome. These profile C infants had an upregulated RAGE signalling pathway (FDR <0.005) and higher risk of asthma (17.9% versus 35.6%; adjusted OR 2.49, 95% CI 1.10-5.87). CONCLUSIONS Metatranscriptome and clustering analysis identified biologically distinct metatranscriptome profiles that have differential risks of asthma.
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Affiliation(s)
- Yoshihiko Raita
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Pérez-Losada
- Dept of Biostatistics and Bioinformatics and Computational Biology Institute, The George Washington University, Washington, DC, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Division of Emergency Medicine, Children's National Hospital, Washington, DC, USA
- Dept of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
- Dept of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Division of Infectious Diseases, Children's National Hospital, Washington, DC, USA
| | - Eduardo Castro-Nallar
- Centro de Bioinformática y Biología Integrativa, Universidad Andres Bello, Santiago, Chile
| | - Ignacio Ramos-Tapia
- Centro de Bioinformática y Biología Integrativa, Universidad Andres Bello, Santiago, Chile
| | - Nathaniel Stearrett
- Computational Biology Institute, The George Washington University, Washington, DC, USA
| | - Yury A Bochkov
- Dept of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E Gern
- Dept of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Dept of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jonathan M Mansbach
- Dept of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaozhong Zhu
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kohei Hasegawa
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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10
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FabT, a Bacterial Transcriptional Repressor That Limits Futile Fatty Acid Biosynthesis. Microbiol Mol Biol Rev 2022; 86:e0002922. [PMID: 35726719 DOI: 10.1128/mmbr.00029-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phospholipids are vital membrane constituents that determine cell functions and interactions with the environment. For bacterial pathogens, rapid adjustment of phospholipid composition to changing conditions during infection can be crucial for growth and survival. Fatty acid synthesis (FASII) regulators are central to this process. This review puts the spotlight on FabT, a MarR-family regulator of FASII characterized in streptococci, enterococci, and lactococci. Roles of FabT in virulence, as reported in mouse and nonhuman primate infection models, will be discussed. We present FabT structure, the FabT regulon, and changes in FabT regulation according to growth conditions. A unique feature of FabT concerns its modulation by an unconventional corepressor, acyl-acyl-carrier protein (ACP). Some bacteria express two ACP proteins, which are distinguished by their interactions with endogenous or exogenous fatty acid sources, one of which causes strong FabT repression. This system seems to allow preferred use of environmental fatty acids, thereby saving energy by limiting futile FASII activity. Control of fabT expression and FabT activity link various metabolic pathways to FASII. The various physiological consequences of FabT loss summarized here suggest that FabT has potential as a narrow range therapeutic target.
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11
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Subramanian C, Cuypers MG, Radka CD, White SW, Rock CO. Domain architecture and catalysis of the Staphylococcus aureus fatty acid kinase. J Biol Chem 2022; 298:101993. [PMID: 35490779 PMCID: PMC9136124 DOI: 10.1016/j.jbc.2022.101993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
Fatty acid kinase (Fak) is a two-component enzyme that generates acyl-phosphate for phospholipid synthesis. Fak consists of a kinase domain protein (FakA) that phosphorylates a fatty acid enveloped by a fatty acid binding protein (FakB). The structural basis for FakB function has been established, but little is known about FakA. Here, we used limited proteolysis to define three separate FakA domains: the amino terminal FakA_N, the central FakA_L, and the carboxy terminal FakA_C. The isolated domains lack kinase activity, but activity is restored when FakA_N and FakA_L are present individually or connected as FakA_NL. The X-ray structure of the monomeric FakA_N captures the product complex with ADP and two Mg2+ ions bound at the nucleotide site. The FakA_L domain encodes the dimerization interface along with conserved catalytic residues Cys240, His282, and His284. AlphaFold analysis of FakA_L predicts the catalytic residues are spatially clustered and pointing away from the dimerization surface. Furthermore, the X-ray structure of FakA_C shows that it consists of two subdomains that are structurally related to FakB. Analytical ultracentrifugation demonstrates that FakA_C binds FakB, and site-directed mutagenesis confirms that a positively charged wedge on FakB meshes with a negatively charged groove on FakA_C. Finally, small angle X-ray scattering analysis is consistent with freely rotating FakA_N and FakA_C domains tethered by flexible linkers to FakA_L. These data reveal specific roles for the three independently folded FakA protein domains in substrate binding and catalysis.
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Affiliation(s)
- Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maxime G Cuypers
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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12
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Zou Q, Dong H, Zhu L, Cronan JE. The Enterococcus faecalis FabT Transcription Factor Regulates Fatty Acid Biosynthesis in Response to Exogeneous Fatty Acids. Front Microbiol 2022; 13:877582. [PMID: 35547134 PMCID: PMC9083066 DOI: 10.3389/fmicb.2022.877582] [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] [Received: 02/16/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
The phospholipid acyl chains of Enterococcus faecalis can be derived either by de novo synthesis or by incorporation of exogenous fatty acids through the fatty acid kinase complex (Fak)-phosphate acyltransferase (PlsX) pathway. Exogenous fatty acids suppress fatty acid synthesis through the transcriptional repressor FabT, the loss of which eliminated regulation of de novo fatty acid biosynthesis and resulted in decreased incorporation of exogenous unsaturated fatty acids. Purified FabT bound to the promoters of several fatty acid synthesis genes that contain a specific palindromic sequence and binding was enhanced by acylated derivatives of acyl carrier protein B (acyl-AcpB). The loss of the PlsX pathway blocked FabT-dependent transcriptional repression in the presence of oleic acid. Transcriptional repression was partially retained in a E. faecalis ΔacpB strain which showed decreased fatty acid biosynthesis in the presence of exogenous unsaturated fatty acids. The FabT-dependent activity remaining in the ΔacpB strain indicates that acylated derivatives of AcpA were weak enhancers of FabT binding although AcpA is believed to primarily function in de novo fatty acid synthesis.
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Affiliation(s)
- Qi Zou
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Huijuan Dong
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Lei Zhu
- College of Life Sciences, Shandong Agricultural University, Taian, China
| | - John E Cronan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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13
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Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW. Identification of Structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. J Biol Chem 2022; 298:101676. [PMID: 35122790 PMCID: PMC8892158 DOI: 10.1016/j.jbc.2022.101676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/31/2022] Open
Abstract
Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.
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Affiliation(s)
- Jessica M Gullett
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maxime G Cuypers
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R Grace
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chitra Subramanian
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles O Rock
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Stephen W White
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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14
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Parreira de Aquino G, Mendes Gomes MA, Köpke Salinas R, Laranjeira-Silva MF. Lipid and fatty acid metabolism in trypanosomatids. MICROBIAL CELL 2021; 8:262-275. [PMID: 34782859 PMCID: PMC8561143 DOI: 10.15698/mic2021.11.764] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 12/18/2022]
Abstract
Trypanosomiases and leishmaniases are neglected tropical diseases that have been spreading to previously non-affected areas in recent years. Identification of new chemotherapeutics is needed as there are no vaccines and the currently available treatment options are highly toxic and often ineffective. The causative agents for these diseases are the protozoan parasites of the Trypanosomatidae family, and they alternate between invertebrate and vertebrate hosts during their life cycles. Hence, these parasites must be able to adapt to different environments and compete with their hosts for several essential compounds, such as amino acids, vitamins, ions, carbohydrates, and lipids. Among these nutrients, lipids and fatty acids (FAs) are essential for parasite survival. Trypanosomatids require massive amounts of FAs, and they can either synthesize FAs de novo or scavenge them from the host. Moreover, FAs are the major energy source during specific life cycle stages of T. brucei, T. cruzi, and Leishmania. Therefore, considering the distinctive features of FAs metabolism in trypanosomatids, these pathways could be exploited for the development of novel antiparasitic drugs. In this review, we highlight specific aspects of lipid and FA metabolism in the protozoan parasites T. brucei, T. cruzi, and Leishmania spp., as well as the pathways that have been explored for the development of new chemotherapies.
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Affiliation(s)
| | | | - Roberto Köpke Salinas
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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15
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Yoon H, Shaw JL, Haigis MC, Greka A. Lipid metabolism in sickness and in health: Emerging regulators of lipotoxicity. Mol Cell 2021; 81:3708-3730. [PMID: 34547235 PMCID: PMC8620413 DOI: 10.1016/j.molcel.2021.08.027] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022]
Abstract
Lipids play crucial roles in signal transduction, contribute to the structural integrity of cellular membranes, and regulate energy metabolism. Questions remain as to which lipid species maintain metabolic homeostasis and which disrupt essential cellular functions, leading to metabolic disorders. Here, we discuss recent advances in understanding lipid metabolism with a focus on catabolism, synthesis, and signaling. Technical advances, including functional genomics, metabolomics, lipidomics, lipid-protein interaction maps, and advances in mass spectrometry, have uncovered new ways to prioritize molecular mechanisms mediating lipid function. By reviewing what is known about the distinct effects of specific lipid species in physiological pathways, we provide a framework for understanding newly identified targets regulating lipid homeostasis with implications for ameliorating metabolic diseases.
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Affiliation(s)
- Haejin Yoon
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Jillian L Shaw
- Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA.
| | - Anna Greka
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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16
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Kengmo Tchoupa A, Eijkelkamp BA, Peschel A. Bacterial adaptation strategies to host-derived fatty acids. Trends Microbiol 2021; 30:241-253. [PMID: 34218980 DOI: 10.1016/j.tim.2021.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 01/08/2023]
Abstract
Fatty acids (FAs) are potent antimicrobials which hold great promise as viable alternatives or complements to conventional antibiotics. Intriguingly, bacteria are well equipped to use environmental FAs as energy sources and/or building blocks for their membrane lipids. Furthermore, these microbes display a wide array of mechanisms to prevent or mitigate FA toxicity. In this review we discuss strategies that bacteria use to thrive despite extensive exposure to host-derived antimicrobial FAs. We also highlight the altered response of these FA-adapted bacteria to antibiotics. Given the ubiquitous nature of FAs in various host environments, deciphering bacterial adaptation strategies to FAs is of prime importance. This knowledge may pave the way for a rational design of FA-based combination therapies with antibiotics.
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Affiliation(s)
- Arnaud Kengmo Tchoupa
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany; Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
| | - Bart A Eijkelkamp
- Molecular Sciences and Technology, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany; Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
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17
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The Membrane Composition Defines the Spatial Organization and Function of a Major Acinetobacter baumannii Drug Efflux System. mBio 2021; 12:e0107021. [PMID: 34134514 PMCID: PMC8262998 DOI: 10.1128/mbio.01070-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Acinetobacter baumannii is one of the world’s most problematic nosocomial pathogens. The combination of its intrinsic resistance and ability to acquire resistance markers allow this organism to adjust to antibiotic treatment. Despite being the primary barrier against antibiotic stress, our understanding of the A. baumannii membrane composition and its impact on resistance remains limited. In this study, we explored how the incorporation of host-derived polyunsaturated fatty acids (PUFAs) is associated with increased antibiotic susceptibility. Functional analyses of primary A. baumannii efflux systems indicated that AdeB-mediated antibiotic resistance was impacted by PUFA treatment. Molecular dynamics simulations of AdeB identified a specific morphological disruption of AdeB when positioned in the PUFA-enriched membrane. Collectively, we have shown that PUFAs can impact antibiotic efficacy via a vital relationship with antibiotic efflux pumps. Furthermore, this work has revealed that A. baumannii’s unconditional desire for fatty acids may present a possible weakness in its multidrug resistance capacity.
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18
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Abstract
Membrane lipid homeostasis is required for bacteria to survive in a spectrum of host environments. This homeostasis is achieved by regulation of fatty acid chain length and of the ratio of unsaturated to saturated fatty acids. In the pathogen Streptococcus pneumoniae, fatty acid biosynthesis is carried out by a cluster of fatty acid biosynthesis (fab) genes (FASII locus) whose expression is controlled by the FabT repressor. Encoded immediately downstream of the FASII locus is BriC, a competence-induced, cell-cell communication peptide that promotes biofilm development as well as nasopharyngeal colonization in a murine model of pneumococcal carriage. Here, we demonstrate that briC is cotranscribed with genes of the fab gene cluster and that a reduction of briC levels, caused by decoupling its transcription from fab gene cluster, negatively affects biofilm development. BriC elevates fabT transcription, which is predicted to alter the balance of unsaturated and saturated fatty acids produced by the pathway. We find that briC inactivation results in a decreased production of unsaturated fatty acids. This affects the membrane properties by decreasing the abundance of di-unsaturated phosphatidylglycerol molecular species. We propose that the link between BriC, FabT, and phospholipid composition contributes to the ability of S. pneumoniae to alter membrane homeostasis in response to the production of a quorum-sensing peptide. IMPORTANCE Adaptation of bacteria to their host environment is a key component of colonization and pathogenesis. As an essential component of bacterial membranes, fatty acid composition contributes to host adaptation. Similarly, cell-cell communication, which enables population level responses, also contributes to host adaptation. While much is known about the pathways that control the biosynthesis of fatty acids, many questions remain regarding regulation of these pathways and consequently the factors that affect the balance between unsaturated and saturated fatty acids. We find that BriC, a cell-cell communication peptide implicated in biofilm regulation and colonization, both is influenced by a fatty acid biosynthesis pathway and affects this same pathway. This study identifies a link between cell-cell communication, fatty acid composition, and biofilms and, in doing so, suggests that these pathways are integrated into the networks that control pneumococcal colonization and host adaptation.
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19
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Woodall BM, Harp JR, Brewer WT, Tague ED, Campagna SR, Fozo EM. Enterococcus faecalis Readily Adapts Membrane Phospholipid Composition to Environmental and Genetic Perturbation. Front Microbiol 2021; 12:616045. [PMID: 34093456 PMCID: PMC8177052 DOI: 10.3389/fmicb.2021.616045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/15/2021] [Indexed: 11/22/2022] Open
Abstract
The bacterial lipid membrane, consisting both of fatty acid (acyl) tails and polar head groups, responds to changing conditions through alteration of either the acyl tails and/or head groups. This plasticity is critical for cell survival as it allows maintenance of both the protective nature of the membrane as well as functioning membrane protein complexes. Bacteria that live in fatty-acid rich environments, such as those found in the human host, can exploit host fatty acids to synthesize their own membranes, in turn, altering their physiology. Enterococcus faecalis is such an organism: it is a commensal of the mammalian intestine where it is exposed to fatty-acid rich bile, as well as a major cause of hospital infections during which it is exposed to fatty acid containing-serum. Within, we employed an untargeted approach to detect the most common phospholipid species of E. faecalis OG1RF via ultra-high performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS). We examined not only how the composition responds upon exposure to host fatty acids but also how deletion of genes predicted to synthesize major polar head groups impact lipid composition. Regardless of genetic background and differing basal lipid composition, all strains were able to alter their lipid composition upon exposure to individual host fatty acids. Specific gene deletion strains, however, had altered survival to membrane damaging agents. Combined, the enterococcal lipidome is highly resilient in response to both genetic and environmental perturbation, likely contributing to stress survival.
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Affiliation(s)
- Brittni M. Woodall
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - John R. Harp
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - William T. Brewer
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric D. Tague
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN, United States
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Elizabeth M. Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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20
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Lannes-Costa PS, de Oliveira JSS, da Silva Santos G, Nagao PE. A current review of pathogenicity determinants of Streptococcus sp. J Appl Microbiol 2021; 131:1600-1620. [PMID: 33772968 DOI: 10.1111/jam.15090] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 12/16/2022]
Abstract
The genus Streptococcus comprises important pathogens, many of them are part of the human or animal microbiota. Advances in molecular genetics, taxonomic approaches and phylogenomic studies have led to the establishment of at least 100 species that have a severe impact on human health and are responsible for substantial economic losses to agriculture. The infectivity of the pathogens is linked to cell-surface components and/or secreted virulence factors. Bacteria have evolved sophisticated and multifaceted adaptation strategies to the host environment, including biofilm formation, survival within professional phagocytes, escape the host immune response, amongst others. This review focuses on virulence mechanism and zoonotic potential of Streptococcus species from pyogenic (S. agalactiae, S. pyogenes) and mitis groups (S. pneumoniae).
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Affiliation(s)
- P S Lannes-Costa
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - J S S de Oliveira
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - G da Silva Santos
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - P E Nagao
- Laboratory of Molecular Biology and Physiology of Streptococci, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
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21
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Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, Hassan KA. Physiological Functions of Bacterial "Multidrug" Efflux Pumps. Chem Rev 2021; 121:5417-5478. [PMID: 33761243 DOI: 10.1021/acs.chemrev.0c01226] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.
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Affiliation(s)
- Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Claire Maher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Liam D H Elbourne
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Ian T Paulsen
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
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22
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Sanchez-Rosario Y, Johnson MDL. Media Matters, Examining Historical and Modern Streptococcus pneumoniae Growth Media and the Experiments They Affect. Front Cell Infect Microbiol 2021; 11:613623. [PMID: 33834003 PMCID: PMC8021847 DOI: 10.3389/fcimb.2021.613623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/02/2021] [Indexed: 12/18/2022] Open
Abstract
While some bacteria can thrive for generations in minerals and salts, many require lavish nutrition and specific chemicals to survive to the point where they can be observed and researched. Although researchers once boiled and rendered animal flesh and bones to obtain a media that facilitated bacterial growth, we now have a plethora of formulations and manufacturers to provide dehydrated flavors of historical, modified, and modern media. The purpose of media has evolved from simple isolation to more measured study. However, in some instances, media formulated to aid the metabolic, nutritional, or physical properties of microbes may not be best suited for studying pathogen behavior or resilience as a function of host interactions. While there have been comparative studies on handfuls of these media in Streptococcus pneumoniae, this review focuses on describing both the historical and modern composition of common complex (Todd Hewitt and M17), semi-defined (Adams and Roe), and defined pneumococcal media (RPMI and Van de Rijn and Kessler), key components discovered/needed for cultivation/growth enhancement, and effects these different media have on bacterial phenotypes and experimental outcomes. While many researchers find the best conditions to grow and experiment on their bacteria of choice, the reasons for some researchers to use a specific medium is at best, not discussed, and at worst, arbitrary. As such, the goal of this review is to highlight the differences in pneumococcal media to encourage investigators to challenge their decisions on why they use a given medium, discuss the recipe, and explain their reasoning.
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Affiliation(s)
| | - Michael D L Johnson
- Department of Immunobiology, University of Arizona, Tucson, AZ, United States.,BIO5 Institute, University of Arizona, Tucson, AZ, United States.,Valley Fever Center for Excellence, University of Arizona, Tucson, AZ, United States
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23
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The Bactericidal Fatty Acid Mimetic 2CCA-1 Selectively Targets Pneumococcal Extracellular Polyunsaturated Fatty Acid Metabolism. mBio 2020; 11:mBio.03027-20. [PMID: 33323510 PMCID: PMC7773995 DOI: 10.1128/mbio.03027-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Fatty acid biosynthesis is an attractive antibiotic target, as it affects the supply of membrane phospholipid building blocks. In Streptococcus pneumoniae, it is not sufficient to target only the endogenous fatty acid synthesis machinery, as uptake of host fatty acids may bypass this inhibition. Streptococcus pneumoniae, a major cause of pneumonia, sepsis, and meningitis worldwide, has the nasopharynges of small children as its main ecological niche. Depletion of pneumococci from this niche would reduce the disease burden and could be achieved using small molecules with narrow-spectrum antibacterial activity. We identified the alkylated dicyclohexyl carboxylic acid 2CCA-1 as a potent inducer of autolysin-mediated lysis of S. pneumoniae, while having low activity against Staphylococcus aureus. 2CCA-1-resistant strains were found to have inactivating mutations in fakB3, known to be required for uptake of host polyunsaturated fatty acids, as well as through inactivation of the transcriptional regulator gene fabT, vital for endogenous, de novo fatty acid synthesis regulation. Structure activity relationship exploration revealed that, besides the central dicyclohexyl group, the fatty acid-like structural features of 2CCA-1 were essential for its activity. The lysis-inducing activity of 2CCA-1 was considerably more potent than that of free fatty acids and required growing bacteria, suggesting that 2CCA-1 needs to be metabolized to exert its antimicrobial activity. Total lipid analysis of 2CCA-1 treated bacteria identified unique masses that were modeled to 2CCA-1 containing lysophosphatidic and phosphatidic acid in wild-type but not in fakB3 mutant bacteria. This suggests that 2CCA-1 is metabolized as a fatty acid via FakB3 and utilized as a phospholipid building block, leading to accumulation of toxic phospholipid species. Analysis of FabT-mediated fakB3 expression elucidates how the pneumococcus could ensure membrane homeostasis and concurrent economic use of host-derived fatty acids.
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24
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Neville SL, Eijkelkamp BA, Lothian A, Paton JC, Roberts BR, Rosch JW, McDevitt CA. Cadmium stress dictates central carbon flux and alters membrane composition in Streptococcus pneumoniae. Commun Biol 2020; 3:694. [PMID: 33214631 PMCID: PMC7678824 DOI: 10.1038/s42003-020-01417-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Metal ion homeostasis is essential for all forms of life. However, the breadth of intracellular impacts that arise upon dysregulation of metal ion homeostasis remain to be elucidated. Here, we used cadmium, a non-physiological metal ion, to investigate how the bacterial pathogen, Streptococcus pneumoniae, resists metal ion stress and dyshomeostasis. By combining transcriptomics, metabolomics and metalloproteomics, we reveal that cadmium stress dysregulates numerous essential cellular pathways including central carbon metabolism, lipid membrane biogenesis and homeostasis, and capsule production at the transcriptional and/or functional level. Despite the breadth of cellular pathways susceptible to metal intoxication, we show that S. pneumoniae is able to maintain viability by utilizing cellular pathways that are predominately metal-independent, such as the pentose phosphate pathway to maintain energy production. Collectively, this work provides insight into the cellular processes impacted by cadmium and how resistance to metal ion toxicity is achieved in S. pneumoniae. Neville et al. investigate how Streptococcus pneumoniae mitigates metal ion stress. Despite cadmium induced dysregulation of central carbon metabolism and lipid membrane homeostasis, they find that S. pneumoniae can remain viable by selectively utilizing predominately metal-independent cellular pathways. This study provides insights into how bacteria overcome metal ion toxicity.
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Affiliation(s)
- Stephanie L Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Amber Lothian
- Melbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Blaine R Roberts
- Melbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
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25
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Induction of Daptomycin Tolerance in Enterococcus faecalis by Fatty Acid Combinations. Appl Environ Microbiol 2020; 86:AEM.01178-20. [PMID: 32801181 PMCID: PMC7531955 DOI: 10.1128/aem.01178-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022] Open
Abstract
With an increasing prevalence of antibiotic resistance in the clinic, we strive to understand more about microbial defensive mechanisms. A nongenetic tolerance to the antibiotic daptomycin was discovered in Enterococcus faecalis that results in the increased survival of bacterial populations after treatment with the drug. This tolerance mechanism likely synergizes with antibiotic resistance in the clinic. Given that this tolerance phenotype is induced by incorporation of fatty acids present in the host, it can be assumed that infections by this organism require a higher dose of antibiotic for successful eradication. The mixture of fatty acids in human fluids is quite diverse, with little understanding between the interplay of fatty acid combinations and the tolerance phenotype we observe. It is crucial to understand the effects of fatty acid combinations on E. faecalis physiology if we are to suppress the tolerance physiology in the clinic. Enterococcus faecalis is a Gram-positive bacterium that normally exists as an intestinal commensal in humans but is also a leading cause of nosocomial infections. Previous work noted that growth supplementation with serum induced tolerance to membrane-damaging agents, including the antibiotic daptomycin. Specific fatty acids found within serum could independently provide tolerance to daptomycin (protective fatty acids), yet some fatty acids found in serum did not and had negative effects on enterococcal physiology (nonprotective fatty acids). Here, we measured a wide array of physiological responses after supplementation with combinations of protective and nonprotective fatty acids to better understand how serum induces daptomycin tolerance. When cells were supplemented with either nonprotective fatty acid, palmitic acid, or stearic acid, there were marked defects in growth and morphology, but these defects were rescued upon supplementation with either protective fatty acid, oleic acid, or linoleic acid. Membrane fluidity decreased with growth in either palmitic or stearic acid alone but returned to basal levels when a protective fatty acid was supplied. Daptomycin tolerance could be induced if a protective fatty acid was provided with a nonprotective fatty acid, and some specific combinations protected as well as serum supplementation. While cell envelope charge has been associated with tolerance to daptomycin in other Gram-positive bacteria, we concluded that it does not correlate with the fatty acid-induced protection we observed. Based on these observations, we conclude that daptomycin tolerance by serum is driven by specific, protective fatty acids found within the fluid. IMPORTANCE With an increasing prevalence of antibiotic resistance in the clinic, we strive to understand more about microbial defensive mechanisms. A nongenetic tolerance to the antibiotic daptomycin was discovered in Enterococcus faecalis that results in the increased survival of bacterial populations after treatment with the drug. This tolerance mechanism likely synergizes with antibiotic resistance in the clinic. Given that this tolerance phenotype is induced by incorporation of fatty acids present in the host, it can be assumed that infections by this organism require a higher dose of antibiotic for successful eradication. The mixture of fatty acids in human fluids is quite diverse, with little understanding between the interplay of fatty acid combinations and the tolerance phenotype we observe. It is crucial to understand the effects of fatty acid combinations on E. faecalis physiology if we are to suppress the tolerance physiology in the clinic.
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Toelzer C, Gupta K, Yadav SKN, Borucu U, Davidson AD, Kavanagh Williamson M, Shoemark DK, Garzoni F, Staufer O, Milligan R, Capin J, Mulholland AJ, Spatz J, Fitzgerald D, Berger I, Schaffitzel C. Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein. Science 2020; 370:725-730. [PMID: 32958580 PMCID: PMC8050947 DOI: 10.1126/science.abd3255] [Citation(s) in RCA: 269] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022]
Abstract
Many efforts to develop therapies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are focused on the spike (S) protein trimer that binds to the host receptor. Structures of trimeric S protein show its receptor-binding domain in either an up or a down conformation. Toelzer et al. produced SARS-CoV-2 S in insect cells and determined the structure by cryo–electron microscopy. In their dataset, the closed form was predominant and was stabilized by binding linoleic acid, an essential fatty acid. A similar binding pocket appears to be present in previous highly pathogenic coronaviruses, and past studies suggested links between viral infection and fatty acid metabolism. The pocket could be exploited to develop inhibitors that trap S protein in the closed conformation. Science, this issue p. 725 Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms that drive high infectivity, broad tissue tropism, and severe pathology. Our 2.85-angstrom cryo–electron microscopy structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains tightly bind the essential free fatty acid linoleic acid (LA) in three composite binding pockets. A similar pocket also appears to be present in the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). LA binding stabilizes a locked S conformation, resulting in reduced angiotensin-converting enzyme 2 (ACE2) interaction in vitro. In human cells, LA supplementation synergizes with the COVID-19 drug remdesivir, suppressing SARS-CoV-2 replication. Our structure directly links LA and S, setting the stage for intervention strategies that target LA binding by SARS-CoV-2.
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Affiliation(s)
- Christine Toelzer
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK
| | - Kapil Gupta
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK
| | - Sathish K N Yadav
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK
| | - Ufuk Borucu
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK
| | - Frederic Garzoni
- Imophoron Ltd., St. Philips Central, Albert Rd., St. Philips, Bristol BS2 0XJ, UK
| | - Oskar Staufer
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany.,Institute for Physical Chemistry, Department for Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany.,Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Rachel Milligan
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Julien Capin
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK
| | - Adrian J Mulholland
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Joachim Spatz
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany.,Institute for Physical Chemistry, Department for Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany.,Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK
| | - Daniel Fitzgerald
- Geneva Biotech Sàrl, Avenue de la Roseraie 64, 1205, Geneva, Switzerland
| | - Imre Berger
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK. .,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK.,Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK.,School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK. .,Bristol Synthetic Biology Centre BrisSynBio, 24 Tyndall Ave., Bristol BS8 1TQ, UK
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