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Yu T, Xu X, Liu Y, Wang X, Wu S, Qiu Z, Liu X, Pan X, Gu C, Wang S, Dong L, Li W, Yao X. Multi-omics signatures reveal genomic and functional heterogeneity of Cutibacterium acnes in normal and diseased skin. Cell Host Microbe 2024; 32:1129-1146.e8. [PMID: 38936370 DOI: 10.1016/j.chom.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/19/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
Cutibacterium acnes is the most abundant bacterium of the human skin microbiome since adolescence, participating in both skin homeostasis and diseases. Here, we demonstrate individual and niche heterogeneity of C. acnes from 1,234 isolate genomes. Skin disease (atopic dermatitis and acne) and body site shape genomic differences of C. acnes, stemming from horizontal gene transfer and selection pressure. C. acnes harbors characteristic metabolic functions, fewer antibiotic resistance genes and virulence factors, and a more stable genome compared with Staphylococcus epidermidis. Integrated genome, transcriptome, and metabolome analysis at the strain level unveils the functional characteristics of C. acnes. Consistent with the transcriptome signature, C. acnes in a sebum-rich environment induces toxic and pro-inflammatory effects on keratinocytes. L-carnosine, an anti-oxidative stress metabolite, is up-regulated in the C. acnes metabolome from atopic dermatitis and attenuates skin inflammation. Collectively, our study reveals the joint impact of genes and the microenvironment on C. acnes function.
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Affiliation(s)
- Tianze Yu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaoqiang Xu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yang Liu
- 01life Institute, Shenzhen 518000, China
| | - Xiaokai Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Shi Wu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhuoqiong Qiu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaochun Liu
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Xiaoyu Pan
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Chaoying Gu
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Shangshang Wang
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lixin Dong
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China.
| | - Wei Li
- Department of Dermatology, Shanghai Institute of Dermatology, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Xu Yao
- Department of Allergy and Rheumatology, Hospital for Skin Diseases, Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China.
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Schiaffi V, Barras F, Bouveret E. Matching the β-oxidation gene repertoire with the wide diversity of fatty acids. Curr Opin Microbiol 2024; 77:102402. [PMID: 37992547 DOI: 10.1016/j.mib.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/24/2023]
Abstract
Bacteria can use fatty acids (FAs) from their environment as carbon and energy source. This catabolism is performed by the enzymes of the well-known β-oxidation machinery, producing reducing power and releasing acetyl-CoA that can feed the tricarboxylic acid cycle. FAs are extremely diverse: they can be saturated or (poly)unsaturated and are found in different sizes. The need to degrade such a wide variety of compounds may explain why so many seemingly homologous enzymes are found for each step of the β-oxidation cycle. In addition, the degradation of unsaturated fatty acids requires specific auxiliary enzymes for isomerase and reductase reactions. Furthermore, the β-oxidation cycle can be blocked by dead-end products, which are taken care of by acyl-CoA thioesterases. Yet, the functional characterization of the enzymes required for the degradation of the full diversity of FAs remains to be documented in most bacteria.
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Affiliation(s)
- Veronica Schiaffi
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France
| | - Frédéric Barras
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France
| | - Emmanuelle Bouveret
- Institut Pasteur, Department of Microbiology, Université Paris-Cité, UMR CNRS 6047, SAMe Unit, France.
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Wilkins AA, Schwarz B, Torres-Escobar A, Castore R, Landry L, Latimer B, Bohrnsen E, Bosio CM, Dragoi AM, Ivanov SS. The intracellular growth of the vacuolar pathogen Legionella pneumophila is dependent on the acyl chain composition of host membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567753. [PMID: 38045297 PMCID: PMC10690232 DOI: 10.1101/2023.11.19.567753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Legionella pneumophila is an accidental human bacterial pathogen that infects and replicates within alveolar macrophages causing a severe atypical pneumonia known as Legionnaires' disease. As a prototypical vacuolar pathogen L. pneumophila establishes a unique endoplasmic reticulum (ER)-derived organelle within which bacterial replication takes place. Bacteria-derived proteins are deposited in the host cytosol and in the lumen of the pathogen-occupied vacuole via a type IVb (T4bSS) and a type II (T2SS) secretion system respectively. These secretion system effector proteins manipulate multiple host functions to facilitate intracellular survival of the bacteria. Subversion of host membrane glycerophospholipids (GPLs) by the internalized bacteria via distinct mechanisms feature prominently in trafficking and biogenesis of the Legionella -containing vacuole (LCV). Conventional GPLs composed of a glycerol backbone linked to a polar headgroup and esterified with two fatty acids constitute the bulk of membrane lipids in eukaryotic cells. The acyl chain composition of GPLs dictates phase separation of the lipid bilayer and therefore determines the physiochemical properties of biological membranes - such as membrane disorder, fluidity and permeability. In mammalian cells, fatty acids esterified in membrane GPLs are sourced endogenously from de novo synthesis or via internalization from the exogenous pool of lipids present in serum and other interstitial fluids. Here, we exploited the preferential utilization of exogenous fatty acids for GPL synthesis by macrophages to reprogram the acyl chain composition of host membranes and investigated its impact on LCV homeostasis and L. pneumophila intracellular replication. Using saturated fatty acids as well as cis - and trans - isomers of monounsaturated fatty acids we discovered that under conditions promoting lipid packing and membrane rigidification L. pneumophila intracellular replication was significantly reduced. Palmitoleic acid - a C16:1 monounsaturated fatty acid - that promotes membrane disorder when enriched in GPLs significantly increased bacterial replication within human and murine macrophages but not in axenic growth assays. Lipidome analysis of infected macrophages showed that treatment with exogenous palmitoleic acid resulted in membrane acyl chain reprogramming in a manner that promotes membrane disorder and live-cell imaging revealed that the consequences of increasing membrane disorder impinge on several LCV homeostasis parameters. Collectively, we provide experimental evidence that L. pneumophila replication within its intracellular niche is a function of the lipid bilayer disorder and hydrophobic thickness.
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Cho SH, Dekoninck K, Collet JF. Envelope-Stress Sensing Mechanism of Rcs and Cpx Signaling Pathways in Gram-Negative Bacteria. J Microbiol 2023; 61:317-329. [PMID: 36892778 DOI: 10.1007/s12275-023-00030-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 03/10/2023]
Abstract
The global public health burden of bacterial antimicrobial resistance (AMR) is intensified by Gram-negative bacteria, which have an additional membrane, the outer membrane (OM), outside of the peptidoglycan (PG) cell wall. Bacterial two-component systems (TCSs) aid in maintaining envelope integrity through a phosphorylation cascade by controlling gene expression through sensor kinases and response regulators. In Escherichia coli, the major TCSs defending cells from envelope stress and adaptation are Rcs and Cpx, which are aided by OM lipoproteins RcsF and NlpE as sensors, respectively. In this review, we focus on these two OM sensors. β-Barrel assembly machinery (BAM) inserts transmembrane OM proteins (OMPs) into the OM. BAM co-assembles RcsF, the Rcs sensor, with OMPs, forming the RcsF-OMP complex. Researchers have presented two models for stress sensing in the Rcs pathway. The first model suggests that LPS perturbation stress disassembles the RcsF-OMP complex, freeing RcsF to activate Rcs. The second model proposes that BAM cannot assemble RcsF into OMPs when the OM or PG is under specific stresses, and thus, the unassembled RcsF activates Rcs. These two models may not be mutually exclusive. Here, we evaluate these two models critically in order to elucidate the stress sensing mechanism. NlpE, the Cpx sensor, has an N-terminal (NTD) and a C-terminal domain (CTD). A defect in lipoprotein trafficking results in NlpE retention in the inner membrane, provoking the Cpx response. Signaling requires the NlpE NTD, but not the NlpE CTD; however, OM-anchored NlpE senses adherence to a hydrophobic surface, with the NlpE CTD playing a key role in this function.
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Affiliation(s)
- Seung-Hyun Cho
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium. .,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.
| | - Kilian Dekoninck
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.,University of California, Berkeley, CA, 94720, USA
| | - Jean-Francois Collet
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium
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Tamothran AM, Bhubalan K, Anuar ST, Curtis JM. The degradation and toxicity of commercially traded vegetable oils following spills in aquatic environment. ENVIRONMENTAL RESEARCH 2022; 214:113985. [PMID: 35970378 DOI: 10.1016/j.envres.2022.113985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
The production of commodity and specialty vegetable oils is increasing every year to fulfill the ever-increasing demand where the trading of oils occurs primarily via sea shipping. Spills of vegetable oil into the aquatic environment may result in detrimental effects on aquatic ecosystems. Environmental degradation of vegetable oil spills occurs mainly via microbial activity, chemical oxidation, wave and wind actions. However, the polymerization of oils can hinder their ability to naturally degrade. Thus, human intervention in the form of both short- and long-term remediation, is desirable to reduce the effects of vegetable oil spills on aquatic ecosystems. Studies have been conducted to determine how the type and concentration of the vegetable oil contamination influence its toxicity on various organisms. Some studies show that the effect of vegetable oil spills is found to be relatively short-lived and to a certain extent increase the survivability of certain organisms. However, the integrated effect of vegetable oil spills on aquatic organisms and their environment is still being researched. This review summarizes the existing knowledge on the reported occurrences of vegetable oil spills, their degradation, and their toxicity towards the surrounding aquatic environment which would be helpful in the knowledge transfer of remediation of vegetable oils.
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Affiliation(s)
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Ocean Pollution and Ecotoxicology Research Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Sabiqah Tuan Anuar
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Jonathan M Curtis
- Lipid Chemistry Group, Dept. of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
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Kang J, Zhou X, Zhang W, Pei F, Ge J. Transcriptomic analysis of bacteriocin synthesis and stress response in Lactobacillus paracasei HD1.7 under acetic acid stress. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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