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Dramé I, Rossez Y, Krzewinski F, Charbonnel N, Ollivier-Nakusi L, Briandet R, Dague E, Forestier C, Balestrino D. FabR, a regulator of membrane lipid homeostasis, is involved in Klebsiella pneumoniae biofilm robustness. mBio 2024:e0131724. [PMID: 39240091 DOI: 10.1128/mbio.01317-24] [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: 05/01/2024] [Accepted: 08/06/2024] [Indexed: 09/07/2024] Open
Abstract
Biofilm is a dynamic structure from which individual bacteria and micro-aggregates are released to subsequently colonize new niches by either detachment or dispersal. Screening of a transposon mutant library identified genes associated with the alteration of Klebsiella pneumoniae biofilm including fabR, which encodes a transcriptional regulator involved in membrane lipid homeostasis. An isogenic ∆fabR mutant formed more biofilm than the wild-type (WT) strain and its trans-complemented strain. The thick and round aggregates observed with ∆fabR were resistant to extensive washes, unlike those of the WT strain. Confocal microscopy and BioFlux microfluidic observations showed that fabR deletion was associated with biofilm robustness and impaired erosion over time. The genes fabB and yqfA associated with fatty acid metabolism were significantly overexpressed in the ∆fabR strain, in both planktonic and biofilm conditions. Two monounsaturated fatty acids, palmitoleic acid (C16:1) and oleic acid (C18:1), were found in higher proportion in biofilm cells than in planktonic forms, whereas heptadecenoic acid (C17:1) and octadecanoic acid, 11-methoxy (C18:0-OCH3) were found in higher proportion in the planktonic lifestyle. The fabR mutation induced variations in the fatty acid composition, with no clear differences in the amounts of saturated fatty acids (SFA) and unsaturated fatty acids for the planktonic lifestyle but lower SFA in the biofilm form. Atomic force microscopy showed that deletion of fabR is associated with decreased K. pneumoniae cell rigidity in the biofilm lifestyle, as well as a softer, more elastic biofilm with increased cell cohesion compared to the wild-type strain.IMPORTANCEKlebsiella pneumoniae is an opportunistic pathogen responsible for a wide range of nosocomial infections. The success of this pathogen is due to its high resistance to antibiotics and its ability to form biofilms. The molecular mechanisms involved in biofilm formation have been largely described but the dispersal process that releases individual and aggregate cells from mature biofilm is less well documented while it is associated with the colonization of new environments and thus new threats. Using a multidisciplinary approach, we show that modifications of bacterial membrane fatty acid composition lead to variations in the biofilm robustness, and subsequent bacterial detachment and biofilm erosion over time. These results enhance our understanding of the genetic requirements for biofilm formation in K. pneumoniae that affect the time course of biofilm development and the embrittlement step preceding its dispersal that will make it possible to control K. pneumoniae infections.
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Affiliation(s)
- Ibrahima Dramé
- Université Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France
| | - Yannick Rossez
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Frederic Krzewinski
- Université Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | | | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Etienne Dague
- LAAS-CNRS, CNRS, Univeristé de Toulouse, Toulouse, France
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2
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Barbarek SC, Shah R, Paul S, Alvarado G, Appala K, Phillips C, Henderson EC, Strandquist ET, Pokorny A, Singh VK, Gatto C, Dahl JU, Hines KM, Wilkinson BJ. Lipidomics of homeoviscous adaptation to low temperatures in Staphylococcus aureus utilizing exogenous straight-chain unsaturated fatty acids. J Bacteriol 2024; 206:e0018724. [PMID: 38953643 PMCID: PMC11270863 DOI: 10.1128/jb.00187-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024] Open
Abstract
It is well established that Staphylococcus aureus can incorporate exogenous straight-chain unsaturated fatty acids (SCUFAs) into membrane phospho- and glyco-lipids from various sources in supplemented culture media and when growing in vivo during infection. Given the enhancement of membrane fluidity when oleic acid (C18:1Δ9) is incorporated into lipids, we were prompted to examine the effect of medium supplementation with C18:1Δ9 on growth at low temperatures. C18:1Δ9 supported the growth of a cold-sensitive, branched-chain fatty acid (BCFA)-deficient mutant at 12°C. Interestingly, we found similar results in the BCFA-sufficient parental strain, supported by the fact that the incorporation of C18:1Δ9 into the membrane increased membrane fluidity in both strains. We show that the incorporation of C18:1Δ9 and its elongation product C20:1Δ11 into membrane lipids was required for growth stimulation and relied on a functional FakAB incorporation system. Lipidomics analysis of the phosphatidylglycerol and diglycosyldiacylglycerol lipid classes revealed major impacts of C18:1Δ9 and temperature on lipid species. Growth at 12°C in the presence of C18:1Δ9 also led to increased production of the carotenoid pigment staphyloxanthin. The enhancement of growth by C18:1Δ9 is an example of homeoviscous adaptation to low temperatures utilizing an exogenous fatty acid. This may be significant in the growth of S. aureus at low temperatures in foods that commonly contain C18:1Δ9 and other SCUFAs in various forms. IMPORTANCE We show that Staphylococcus aureus can use its known ability to incorporate exogenous fatty acids to enhance its growth at low temperatures. Individual species of phosphatidylglycerols and diglycosyldiacylglycerols bearing one or two degrees of unsaturation derived from the incorporation of C18:1Δ9 at 12°C are described for the first time. In addition, enhanced production of the carotenoid staphyloxanthin occurs at low temperatures. The studies describe a biochemical reality underlying membrane biophysics. This is an example of homeoviscous adaptation to low temperatures utilizing exogenous fatty acids over the regulation of the biosynthesis of endogenous fatty acids. The studies have likely relevance to food safety in that unsaturated fatty acids may enhance the growth of S. aureus in the food environment.
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Affiliation(s)
- Shannon C. Barbarek
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Ritika Shah
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Sharanya Paul
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Gloria Alvarado
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Keerthi Appala
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Caiden Phillips
- Department of Microbiology and Immunology, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Emma C. Henderson
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Evan T. Strandquist
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Antje Pokorny
- Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, North Carolina, USA
| | - Vineet K. Singh
- Department of Microbiology and Immunology, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Craig Gatto
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Jan-Ulrik Dahl
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Kelly M. Hines
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Brian J. Wilkinson
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
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3
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Rahn HP, Sun J, Li Z, Waymouth RM, Levy R, Wender PA. Isoprenoid CARTs: In Vitro and In Vivo mRNA Delivery by Charge-Altering Releasable Transporters Functionalized with Archaea-inspired Branched Lipids. Biomacromolecules 2024; 25:4305-4316. [PMID: 38814265 DOI: 10.1021/acs.biomac.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The delivery of oligonucleotides across biological barriers is a challenge of unsurpassed significance at the interface of materials science and medicine, with emerging clinical utility in prophylactic and therapeutic vaccinations, immunotherapies, genome editing, and cell rejuvenation. Here, we address the role of readily available branched lipids in the design, synthesis, and evaluation of isoprenoid charge-altering releasable transporters (CARTs), a pH-responsive oligomeric nanoparticle delivery system for RNA. Systematic variation of the lipid block reveals an emergent relationship between the lipid block and the neutralization kinetics of the polycationic block. Unexpectedly, iA21A11, a CART with the smallest lipid side chain, isoamyl-, was identified as the lead isoprenoid CART for the in vitro transfection of immortalized lymphoblastic cell lines. When administered intramuscularly in a murine model, iA21A11-mRNA complexes induce higher protein expression levels than our previous lead CART, ONA. Isoprenoid CARTs represent a new delivery platform for RNA vaccines and other polyanion-based therapeutics.
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Affiliation(s)
- Harrison P Rahn
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jiuzhi Sun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Zhijian Li
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Robert M Waymouth
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ronald Levy
- Stanford Cancer Institute, Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, United States
| | - Paul A Wender
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
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4
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van Aalst EJ, Yekefallah M, A M van Beekveld R, Breukink E, Weingarth M, Wylie BJ. Coordination of bilayer properties by an inward-rectifier K + channel is a cooperative process driven by protein-lipid interaction. J Struct Biol X 2024; 9:100101. [PMID: 38883399 PMCID: PMC11176924 DOI: 10.1016/j.yjsbx.2024.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Physical properties of biological membranes directly or indirectly govern biological processes. Yet, the interplay between membrane and integral membrane proteins is difficult to assess due to reciprocal effects between membrane proteins, individual lipids, and membrane architecture. Using solid-state NMR (SSNMR) we previously showed that KirBac1.1, a bacterial Inward-Rectifier K+ channel, nucleates bilayer ordering and microdomain formation through tethering anionic lipids. Conversely, these lipids cooperatively bind cationic residues to activate the channel and initiate K+ flux. The mechanistic details governing the relationship between cooperative lipid loading and bilayer ordering are, however, unknown. To investigate, we generated KirBac1.1 samples with different concentrations of 13C-lableded phosphatidyl glycerol (PG) lipids and acquired a full suite of SSNMR 1D temperature series experiments using the ordered all-trans (AT) and disordered trans-gauche (TG) acyl conformations as markers of bilayer dynamics. We observed increased AT ordered signal, decreased TG disordered signal, and increased bilayer melting temperature with increased PG concentration. Further, we identified cooperativity between ordering and direct binding of PG lipids, indicating KirBac1.1-driven bilayer ordering and microdomain formation is a classically cooperative Hill-type process driven by and predicated upon direct binding of PG lipids. Our results provide unique mechanistic insight into how proteins and lipids in tandem contribute to supramolecular bilayer heterogeneity in the lipid membrane.
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Affiliation(s)
- Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Roy A M van Beekveld
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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Stubb H, Viitaja T, Trevorah RM, Raitanen JE, Moilanen J, Svedström KJ, Ekholm FS. Another Brick in the Wall of Tear Film Insights Added Through the Total Synthesis and Biophysical Profiling of anteiso-Branched Wax and Cholesteryl Esters. JOURNAL OF NATURAL PRODUCTS 2024; 87:954-965. [PMID: 38547477 PMCID: PMC11389978 DOI: 10.1021/acs.jnatprod.3c01247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
The tear film lipid layer (TFLL) plays a vital part in maintenance of ocular health and represents a unique biological barrier comprising unusual and specialized lipid classes and species. The wax and cholesteryl esters (WEs and CEs) constitute roughly 80-90% of the TFLL. The majority of species in these lipid classes are branched and it is therefore surprising that the synthesis and properties of the second largest category of species, i.e., the anteiso-branched species, remain poorly characterized. In this study, we have developed a total synthesis route and completed a detailed NMR spectroscopic characterization of two common anteiso-branched species, namely: (22S)-22-methyltetracosanyl oleate and cholesteryl (22'S)-22'-methyltetracosanoate. In addition, we have studied their structural properties in the bulk state by wide-angle and small-angle X-ray scattering and their behavior at the aqueous interface using Langmuir monolayer techniques. A comparison to the properties displayed by iso-branched and straight-chain analogues indicate that branching patterns lead to distinct properties in the CE and WE lipid classes. Overall, this study complements the previous work in the field and adds another important brick in the tear film insights wall.
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Affiliation(s)
- Henrik Stubb
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Tuomo Viitaja
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
- Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, FI-00290 Helsinki, Finland
| | - Ryan M Trevorah
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Jan-Erik Raitanen
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Jukka Moilanen
- Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, FI-00290 Helsinki, Finland
| | - Kirsi J Svedström
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Filip S Ekholm
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
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6
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Wang D, Hao L, Jiao X, Que Z, Huang J, Jin Y, Zhou R, Wang Z, Wu C. Engineering the synthesis of unsaturated fatty acids by introducing desaturase improved the stress tolerance of yeast. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:2398-2405. [PMID: 37996964 DOI: 10.1002/jsfa.13162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/28/2023] [Accepted: 11/24/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Yeast is often used to build cell factories to produce various chemicals or nutrient substances, which means the yeast has to encounter stressful environments. Previous research reported that unsaturated fatty acids were closely related to yeast stress resistance. Engineering unsaturated fatty acids may be a viable strategy for enhancing the stress resistance of cells. RESULTS In this study, two desaturase genes, OLE1 and FAD2 from Z. rouxii, were overexpressed in S. cerevisiae to determine how unsaturated fatty acids affect cellular stress tolerance of cells. After cloning and plasmid recombination, the recombinant S. cerevisiae cells were constructed. Analysis of membrane fatty acid contents revealed that the recombinant S. cerevisiae with overexpression of OLE1 and FAD2 genes contained higher levels of fatty acids C16:1 (2.77 times), C18:1 (1.51 times) and C18:2 (4.15 times) than the wild-type S. cerevisiae pY15TEF1. In addition, recombinant S. cerevisiae cells were more resistant to multiple stresses, and exhibited improved membrane functionality, including membrane fluidity and integrity. CONCLUSION These findings demonstrated that strengthening the expression of desaturases was beneficial to stress tolerance. Overall, this study may provide a suitable means to build a cell factory of industrial yeast cells with high tolerance during biological manufacturing. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Dingkang Wang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Global Health Institute, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an Jiaotong University, Xian, China
| | - Liying Hao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xue Jiao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Zhiluo Que
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Zhonghui Wang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
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7
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Barbarek SC, Shah R, Paul S, Alvarado G, Appala K, Henderson EC, Strandquist ET, Pokorny A, Singh VK, Gatto C, Dahl JU, Hines KM, Wilkinson BJ. Lipidomics of homeoviscous adaptation to low temperatures in Staphylococcus aureus utilizing exogenous straight-chain unsaturated fatty acids over biosynthesized endogenous branched-chain fatty acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578686. [PMID: 38352554 PMCID: PMC10862916 DOI: 10.1101/2024.02.02.578686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
It is well established that Staphylococcus aureus can incorporate exogenous straight-chain unsaturated fatty acids (SCUFAs) into membrane phospho- and glyco-lipids from various sources in supplemented culture media, and when growing in vivo in an infection. Given the enhancement of membrane fluidity when oleic acid (C18:1Δ9) is incorporated into lipids, we were prompted to examine the effect of medium supplementation with C18:1Δ9 on growth at low temperatures. C18:1Δ9 supported the growth of a cold-sensitive, branched-chain fatty acid (BCFA)-deficient mutant at 12°C. Interestingly, we found similar results in the BCFA-sufficient parental strain. We show that incorporation of C18:1Δ9 and its elongation product C20:1Δ9 into membrane lipids was required for growth stimulation and relied on a functional FakAB incorporation system. Lipidomics analysis of the phosphatidylglycerol (PG) and diglycosyldiacylglycerol (DGDG) lipid classes revealed major impacts of C18:1Δ9 and temperature on lipid species. Growth at 12°C in the presence of C18:1Δ9 also led to increased production of the carotenoid pigment staphyloxanthin; however, this was not an obligatory requirement for cold adaptation. Enhancement of growth by C18:1Δ9 is an example of homeoviscous adaptation to low temperatures utilizing an exogenous fatty acid. This may be significant in the growth of S. aureus at low temperatures in foods that commonly contain C18:1Δ9 and other SCUFAs in various forms.
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Affiliation(s)
| | - Ritika Shah
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Sharanya Paul
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Gloria Alvarado
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Keerthi Appala
- Department of Chemistry, University of Georgia, Athens, GA
| | - Emma C. Henderson
- School of Biological Sciences, Illinois State University, Normal, IL
| | | | - Antje Pokorny
- Department of Chemistry and Biochemistry, University of North Carolina-Wilmington, Wilmington, NC
| | - Vineet K. Singh
- Department of Microbiology and Immunology, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, MO
| | - Craig Gatto
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Jan-Ulrik Dahl
- School of Biological Sciences, Illinois State University, Normal, IL
| | - Kelly M. Hines
- Department of Chemistry, University of Georgia, Athens, GA
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8
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Egas RA, Sahonero-Canavesi DX, Bale NJ, Koenen M, Yildiz Ç, Villanueva L, Sousa DZ, Sánchez-Andrea I. Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans. Environ Microbiol 2024; 26:e16565. [PMID: 38356112 DOI: 10.1111/1462-2920.16565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024]
Abstract
Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.
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Affiliation(s)
- Reinier A Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Çağlar Yildiz
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Environmental Sciences and Sustainability Department, Science & Technology School, IE University, Segovia, Spain
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9
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He Y, Lei JN, Zhu S, Liu YF, Xu YJ. Monomethyl branched-chain fatty acids-a pearl dropped in the ocean. Crit Rev Food Sci Nutr 2023; 64:9045-9057. [PMID: 37140184 DOI: 10.1080/10408398.2023.2207655] [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] [Indexed: 05/05/2023]
Abstract
As an emerging group of bioactive fatty acids, monomethyl branched-chain fatty acids (mmBCFAs) have sparked the interest of many researchers both domestically and internationally. In addition to documenting the importance of mmBCFAs for growth and development, there is increasing evidence that mmBCFAs are highly correlated with obesity and insulin resistance. According to previous pharmacological investigations, mmBCFAs also exhibit anti-inflammatory effects and anticancer properties. This review summarized the distribution of mmBCFAs, which are widely found in dairy products, ruminants, fish, and fermented foods. Besides, we discuss the biosynthesis pathway in different species and detection methods of mmBCFAs. With the hope to unveil their mechanisms of action, we recapitulated detailed the nutrition and health benefits of mmBCFAs. Furthermore, this study provides a thorough, critical overview of the current state of the art, upcoming difficulties, and trends in mmBCFAs.
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Affiliation(s)
- Yuan He
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Jing-Nan Lei
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Shuang Zhu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Yuan-Fa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
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10
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Whaley SG, Frank MW, Rock CO. A short-chain acyl-CoA synthetase that supports branched-chain fatty acid synthesis in Staphylococcus aureus. J Biol Chem 2023; 299:103036. [PMID: 36806679 PMCID: PMC10026030 DOI: 10.1016/j.jbc.2023.103036] [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: 12/19/2022] [Revised: 01/24/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Staphylococcus aureus controls its membrane biophysical properties using branched-chain fatty acids (BCFAs). The branched-chain acyl-CoA precursors, utilized to initiate fatty acid synthesis, are derived from branched-chain ketoacid dehydrogenase (Bkd), a multiprotein complex that converts α-keto acids to their corresponding acyl-CoAs; however, Bkd KO strains still contain BCFAs. Here, we show that commonly used rich medias contain substantial concentrations of short-chain acids, like 2-methylbutyric and isobutyric acids, that are incorporated into membrane BCFAs. Bkd-deficient strains cannot grow in defined medium unless it is supplemented with either 2-methylbutyric or isobutyric acid. We performed a screen of candidate KO strains and identified the methylbutyryl-CoA synthetase (mbcS gene; SAUSA300_2542) as required for the incorporation of 2-methylbutyric and isobutyric acids into phosphatidylglycerol. Our mass tracing experiments show that isobutyric acid is converted to isobutyryl-CoA that flows into the even-chain acyl-acyl carrier protein intermediates in the type II fatty acid biosynthesis elongation cycle. Furthermore, purified MbcS is an ATP-dependent acyl-CoA synthetase that selectively catalyzes the activation of 2-methylbutyrate and isobutyrate. We found that butyrate and isovalerate are poor MbcS substrates and activity was not detected with acetate or short-chain dicarboxylic acids. Thus, MbcS functions to convert extracellular 2-methylbutyric and isobutyric acids to their respective acyl-CoAs that are used by 3-ketoacyl-ACP synthase III (FabH) to initiate BCFA biosynthesis.
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Affiliation(s)
- Sarah G Whaley
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew W Frank
- Department of Infectious Diseases, 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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11
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Modi SK, Gaur S, Sengupta M, Singh MS. Mechanistic insights into nanoparticle surface-bacterial membrane interactions in overcoming antibiotic resistance. Front Microbiol 2023; 14:1135579. [PMID: 37152753 PMCID: PMC10160668 DOI: 10.3389/fmicb.2023.1135579] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
Antimicrobial Resistance (AMR) raises a serious concern as it contributes to the global mortality by 5 million deaths per year. The overall impact pertaining to significant membrane changes, through broad spectrum drugs have rendered the bacteria resistant over the years. The economic expenditure due to increasing drug resistance poses a global burden on healthcare community and must be dealt with immediate effect. Nanoparticles (NP) have demonstrated inherent therapeutic potential or can serve as nanocarriers of antibiotics against multidrug resistant (MDR) pathogens. These carriers can mask the antibiotics and help evade the resistance mechanism of the bacteria. The targeted delivery can be fine-tuned through surface functionalization of Nanocarriers using aptamers, antibodies etc. This review covers various molecular mechanisms acquired by resistant bacteria towards membrane modification. Mechanistic insight on 'NP surface-bacterial membrane' interactions are crucial in deciding the role of NP as therapeutic. Finally, we highlight the potential accessible membrane targets for designing smart surface-functionalized nanocarriers which can act as bacteria-targeted robots over the existing clinically available antibiotics. As the bacterial strains around us continue to evolve into resistant versions, nanomedicine can offer promising and alternative tools in overcoming AMR.
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Affiliation(s)
- Suraj Kumar Modi
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Smriti Gaur
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Mrittika Sengupta
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
- Mrittika Sengupta, ;
| | - Manu Smriti Singh
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
- *Correspondence: Manu Smriti Singh, ;
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12
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Joodaki F, Martin LM, Greenfield ML. Generation and Computational Characterization of a Complex Staphylococcus aureus Lipid Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9481-9499. [PMID: 35901279 DOI: 10.1021/acs.langmuir.2c00483] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Studies indicate a crucial cell membrane role in the antibiotic resistance of Staphylococcus aureus. To simulate its membrane structure and dynamics, a complex molecular-scale computational representation of the S. aureus lipid bilayer was developed. Phospholipid types and their amounts were optimized by reverse Monte Carlo to represent characterization data from the literature, leading to 19 different phospholipid types that combine three headgroups [phosphatidylglycerol, lysyl-phosphatidylglycerol (LPG), and cardiolipin] and 10 tails, including iso- and anteiso-branched saturated chains. The averaged lipid bilayer thickness was 36.7 Å, and area per headgroup was 67.8 Å2. Phosphorus and nitrogen density profiles showed that LPG headgroups tended to be bent and oriented more parallel to the bilayer plane. The water density profile showed that small amounts reached the membrane center. Carbon density profiles indicated hydrophobic interactions for all lipids in the middle of the bilayer. Bond vector order parameters along each tail demonstrated different C-H ordering even within distinct lipids of the same type; however, all tails followed similar trends in average order parameter. These complex simulations further revealed bilayer insights beyond those attainable with monodisperse, unbranched lipids. Longer tails often extended into the opposite leaflet. Carbon at and beyond a branch showed significantly decreased ordering compared to carbon in unbranched tails; this feature arose in every branched lipid. Diverse tail lengths distributed these disordered methyl groups throughout the middle third of the bilayer. Distributions in mobility and ordering reveal diverse properties that cannot be obtained with monodisperse lipids.
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Affiliation(s)
- Faramarz Joodaki
- Department of Chemical Engineering, University of Rhode Island, 360 Fascitelli Center for Advanced Engineering, Kingston, Rhode Island 02881, United States
| | - Lenore M Martin
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Michael L Greenfield
- Department of Chemical Engineering, University of Rhode Island, 360 Fascitelli Center for Advanced Engineering, Kingston, Rhode Island 02881, United States
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13
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Viitaja T, Raitanen JE, Hynynen A, Moilanen J, Svedström K, Paananen RO, Ekholm FS. On the importance of chain branching in tear film lipid layer wax and cholesteryl esters. Colloids Surf B Biointerfaces 2022; 214:112429. [PMID: 35278859 DOI: 10.1016/j.colsurfb.2022.112429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
Abstract
The tear film lipid layer (TFLL) is important to the maintenance of ocular surface health. Surprisingly, information on the individual roles of the myriad of unique lipids found therein is limited. The most abundant lipid species are the wax esters (WE) and cholesteryl esters (CE), and, especially their branched analogs. The isolation of these lipid species from the TFLL has proved to be tedious, and as a result, insights on their biophysical profiles and role in the TFLL is currently lacking. Herein, we circumvent these issues by a total synthesis of the most abundant iso-methyl branched WEs and CEs found in the TFLL. Through a detailed characterization of the biophysical properties, by the use of Langmuir monolayer and wide-angle X-ray scattering techniques, we demonstrate that chain branching alters the behavior of these lipid species on multiple levels. Taken together, our results fill an important knowledge gap concerning the structure and function of the TFLL on the whole.
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Affiliation(s)
- Tuomo Viitaja
- Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki FI-00014, Finland; Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, Helsinki FI-00290, Finland
| | - Jan-Erik Raitanen
- Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki FI-00014, Finland
| | - Antti Hynynen
- Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki FI-00014, Finland
| | - Jukka Moilanen
- Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, Helsinki FI-00290, Finland
| | - Kirsi Svedström
- Department of Physics, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland
| | - Riku O Paananen
- Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki FI-00014, Finland; Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, Helsinki FI-00290, Finland.
| | - Filip S Ekholm
- Department of Chemistry, University of Helsinki, P.O. Box 55, Helsinki FI-00014, Finland.
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14
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Conte G, Dimauro C, Daghio M, Serra A, Mannelli F, McAmmond BM, Van Hamme JD, Buccioni A, Viti C, Mantino A, Mele M. Exploring the relationship between bacterial genera and lipid metabolism in bovine rumen. Animal 2022; 16:100520. [PMID: 35468508 DOI: 10.1016/j.animal.2022.100520] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/01/2022] Open
Abstract
The rumen is characterised by a complex microbial ecosystem, which is particularly active in lipid metabolism. Several studies demonstrated a role of diet and breed on bacterial community profile, with the effect on metabolic pathways. Despite the knowledge achieved on metabolism and the bacterial profile, little is known about the relationship between individual bacteria and metabolic pathways. Therefore, a multivariate approach was used to search for possible relationships between bacteria and products of several pathways. The correlation between rumen bacterial community composition and rumen lipid metabolism was assessed in 40 beef steers (20 Maremmana and 20 Aubrac) reared with the same system and fed the same diet. A canonical discriminant analysis combined with a canonical correlation analysis (CCA) was performed to explore this correlation. The variables showing a Pearson correlation higher than 0.6 as absolute value and significant were retained for CCA considering the relationship of bacterial composition with several metabolic pathways. The results indicated that some bacterial genera could have significant impacts on the presence of several fatty acids. However, the relationship between genera and fatty acid changes according to the breed, demonstrating that the metabolic pathways change according to the host genetic background, related to breed evolution, although there is also an intra-breed genetic background which should not be ignored. In Maremmana, Succiniclasticum and Rikenellaceae_RC9_gut_group showed a high positive correlation with dimethylacetals (DMAs) DMAC13:0, DMAC14:0, DMAC14:0iso, DMAC15:0, DMAC15:0iso, and DMAC18:0. Prevotellaceae_UCG-003 correlates with C18:3c9c12c15 and C18:1t11, while Fibrobacter and Succiniclasticum correlate with C18:2c9t11 and Lachnospiraceae_NK3A20_group correlates with C18:1c12. Prevotellaceae_UCG-003, Ruminococcaceae_UCG-010, and Oribacterium showed a positive correlation with C13:0iso, and C17:0. Conversely, in Aubrac, Treponema_2 and Rikenellaceae_RC9_gut_group correlated with DMAC14:0iso, DMAC16:0iso, DMAC17:0iso, while Ruminococcaceae_UCG-010, Christensenellaceae_R-7_group and Ruminococcaceae_NK4A214_group correlated with DMAC18:1t11, DMAC14:0, DMAC18:1c12. Acetitomaculum correlated with C18:2c9c12, C18:1c12, C18:1c13, C18:1t12 and Lachnospiraceae_NK3A20_group with C18:1t6-8 and C18:1t9. Saccharofermentas, Ruminococcaceae_UCG-010 and Rikenellaceae_RC9_gut_group correlated with C18:2c9t11 while, Prevotellaceae_UCG-001 and Ruminococcus_1 correlated with C14:0iso, C15:0, C15:0iso, C17:0. Saccharofermentans, Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, and Ruminococcaceae_UCG-010 correlated with C13:1c12 and C16:0iso. These results lead to hypothesise a possible association between several metabolic pathways and one or a few bacterial genera. If these associations are confirmed by further investigations that verify the causality of a bacterial genus with a particular metabolic process, it will be possible to deepen the knowledge on the activity of the rumen population in lipid metabolism. This approach appears to be a promising tool for uncovering the correlation between bacterial genera and products of rumen lipid metabolism.
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Affiliation(s)
- G Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - C Dimauro
- Dipartimento di Scienze Agrarie, University of Sassari, Via de Nicola 9, 07100 Sassari, Italy
| | - M Daghio
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy.
| | - A Serra
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - F Mannelli
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy
| | - B M McAmmond
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
| | - J D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
| | - A Buccioni
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy
| | - C Viti
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy
| | - A Mantino
- Istituto di Scienze della Vita, Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
| | - M Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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15
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Elimelech O, Aviv O, Oded M, Peng X, Harries D, Banin U. Entropy of Branching Out: Linear versus Branched Alkylthiols Ligands on CdSe Nanocrystals. ACS NANO 2022; 16:4308-4321. [PMID: 35157440 PMCID: PMC8945696 DOI: 10.1021/acsnano.1c10430] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Surface ligands of semiconductor nanocrystals (NCs) play key roles in determining their colloidal stability and physicochemical properties and are thus enablers also for the NCs flexible manipulation toward numerous applications. Attention is usually paid to the ligand binding group, while the impact of the ligand chain backbone structure is less discussed. Using isothermal titration calorimetry (ITC), we studied the effect of structural changes in the ligand chain on the thermodynamics of the exchange reaction for oleate coated CdSe NCs, comparing linear and branched alkylthiols. The investigated alkylthiol ligands differed in their backbone length, branching position, and branching group length. Compared to linear ligands, lower exothermicity and entropy loss were observed for an exchange with branched ligands, due to steric hindrance in ligand packing, thereby justifying their previous classification as "entropic ligands". Mean-field calculations for ligand binding demonstrate the contribution to the overall entropy originating from ligand conformational entropy, which is diminished upon binding mainly by packing of NC-bound ligands. Model calculations and the experimental ITC data both point to an interplay between the branching position and the backbone length in determining the entropic nature of the branched ligand. Our findings suggest that the most entropic ligand should be a short, branched ligand with short branching group located toward the middle of the ligand chain. The insights provided by this work also contribute to a future smarter NC surface design, which is an essential tool for their implementation in diverse applications.
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Affiliation(s)
- Orian Elimelech
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Aviv
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Meirav Oded
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Xiaogang Peng
- Department
of Chemistry, Zhejiang University, Hangzhou 310027 P. R. China
| | - Daniel Harries
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The
Fritz Haber Center, The Hebrew University
of Jerusalem, Jerusalem 9190401, Israel
| | - Uri Banin
- The
Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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16
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MacDermott-Opeskin HI, Gupta V, O’Mara ML. Lipid-mediated antimicrobial resistance: a phantom menace or a new hope? Biophys Rev 2022; 14:145-162. [PMID: 35251360 PMCID: PMC8880301 DOI: 10.1007/s12551-021-00912-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/14/2021] [Indexed: 02/06/2023] Open
Abstract
Abstract The proposition of a post-antimicrobial era is all the more realistic with the continued rise of antimicrobial resistance. The development of new antimicrobials is failing to counter the ever-increasing rates of bacterial antimicrobial resistance. This necessitates novel antimicrobials and drug targets. The bacterial cell membrane is an essential and highly conserved cellular component in bacteria and acts as the primary barrier for entry of antimicrobials into the cell. Although previously under-exploited as an antimicrobial target, the bacterial cell membrane is attractive for the development of novel antimicrobials due to its importance in pathogen viability. Bacterial cell membranes are diverse assemblies of macromolecules built around a central lipid bilayer core. This lipid bilayer governs the overall membrane biophysical properties and function of its membrane-embedded proteins. This mini-review will outline the mechanisms by which the bacterial membrane causes and controls resistance, with a focus on alterations in the membrane lipid composition, chemical modification of constituent lipids, and the efflux of antimicrobials by membrane-embedded efflux systems. Thorough insight into the interplay between membrane-active antimicrobials and lipid-mediated resistance is needed to enable the rational development of new antimicrobials. In particular, the union of computational approaches and experimental techniques for the development of innovative and efficacious membrane-active antimicrobials is explored.
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Affiliation(s)
- Hugo I. MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Vrinda Gupta
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Megan L. O’Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
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17
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Microbial cell surface engineering for high-level synthesis of bio-products. Biotechnol Adv 2022; 55:107912. [PMID: 35041862 DOI: 10.1016/j.biotechadv.2022.107912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 02/08/2023]
Abstract
Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.
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18
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Frank MW, Whaley SG, Rock CO. Branched-chain amino acid metabolism controls membrane phospholipid structure in Staphylococcus aureus. J Biol Chem 2021; 297:101255. [PMID: 34592315 PMCID: PMC8524195 DOI: 10.1016/j.jbc.2021.101255] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022] Open
Abstract
Branched-chain amino acids (primarily isoleucine) are important regulators of virulence and are converted to precursor molecules used to initiate fatty acid synthesis in Staphylococcus aureus. Defining how bacteria control their membrane phospholipid composition is key to understanding their adaptation to different environments. Here, we used mass tracing experiments to show that extracellular isoleucine is preferentially metabolized by the branched-chain ketoacid dehydrogenase complex, in contrast to valine, which is not efficiently converted to isobutyryl-CoA. This selectivity creates a ratio of anteiso:iso C5-CoAs that matches the anteiso:iso ratio in membrane phospholipids, indicating indiscriminate utilization of these precursors by the initiation condensing enzyme FabH. Lipidomics analysis showed that removal of isoleucine and leucine from the medium led to the replacement of phospholipid molecular species containing anteiso/iso 17- and 19-carbon fatty acids with 18- and 20-carbon straight-chain fatty acids. This compositional change is driven by an increase in the acetyl-CoA:C5-CoA ratio, enhancing the utilization of acetyl-CoA by FabH. The acyl carrier protein (ACP) pool normally consists of odd carbon acyl-ACP intermediates, but when branched-chain amino acids are absent from the environment, there was a large increase in even carbon acyl-ACP pathway intermediates. The high substrate selectivity of PlsC ensures that, in the presence or the absence of extracellular Ile/Leu, the 2-position is occupied by a branched-chain 15-carbon fatty acid. These metabolomic measurements show how the metabolism of isoleucine and leucine, rather than the selectivity of FabH, control the structure of membrane phospholipids.
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Affiliation(s)
- Matthew W Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sarah G Whaley
- Department of Infectious Diseases, 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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19
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Rasouli A, Jamali Y, Tajkhorshid E, Bavi O, Pishkenari HN. Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study. J Mech Behav Biomed Mater 2021; 117:104386. [PMID: 33588213 PMCID: PMC8009841 DOI: 10.1016/j.jmbbm.2021.104386] [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: 07/11/2020] [Revised: 01/03/2021] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was observed between the two. The global properties of the two lipid bilayers are vastly different, with ether bilayer being stiffer, less ordered, and thicker than ester bilayer. Moreover, ether linkage decreased the area per lipid in the ether lipid bilayer. Our computational framework and output demonstrate how ether modification changes the mechano-chemical properties of DPhPC bilayers.
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Affiliation(s)
- Ali Rasouli
- 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, USA
| | - Yousef Jamali
- School of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Emad Tajkhorshid
- 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, USA
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, Iran.
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20
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Santoscoy MC, Jarboe LR. A systematic framework for using membrane metrics for strain engineering. Metab Eng 2021; 66:98-113. [PMID: 33813035 DOI: 10.1016/j.ymben.2021.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 11/20/2022]
Abstract
The cell membrane plays a central role in the fitness and performance of microbial cell factories and therefore it is an attractive engineering target. The goal of this work is to develop a systematic framework for identifying membrane features for use as engineering targets. The metrics that describe the composition of the membrane can be visualized as "knobs" that modulate various "outcomes", such as physical properties of the membrane and metabolic activity in the form of growth and productivity, with these relationships varying depending on the condition. We generated a set of strains with altered membrane lipid composition via expression of des, fabA and fabB and performed a rigorous characterization of these knobs and outcomes across several individual inhibitory conditions. Here, the knobs are the relative abundance of unsaturated lipids and lipids containing cyclic rings; the average lipid length, and the ratio of linear and non-linear lipids (L/nL ratio). The outcomes are membrane permeability, hydrophobicity, fluidity, and specific growth rate. This characterization identified significant correlations between knobs and outcomes that were specific to individual inhibitors, but also were significant across all tested conditions. For example, across all conditions, the L/nL ratio is positively correlated with the cell surface hydrophobicity, and the average lipid length is positively correlated with specific growth rate. A subsequent analysis of the data with the individual inhibitors identified pairs of lipid metrics and membrane properties that were predicted to impact cell growth in seven modeled scenarios with two or more inhibitors. The L/nL ratio and the membrane hydrophobicity were predicted to impact cell growth with the highest frequency. We experimentally validated this prediction in the combined condition of 42 °C, 2.5 mM furfural and 2% v/v ethanol in minimal media. Membrane hydrophobicity was confirmed to be a significant predictor of ethanol production. This work demonstrates that membrane physical properties can be used to predict the performance of biocatalysts in single and multiple inhibitory conditions, and possibly as an engineering target. In this manner, membrane properties can possibly be used as screening or selection metrics for library- or evolution-based strain engineering.
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Affiliation(s)
- Miguel C Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
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21
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Blitzblau HG, Consiglio AL, Teixeira P, Crabtree DV, Chen S, Konzock O, Chifamba G, Su A, Kamineni A, MacEwen K, Hamilton M, Tsakraklides V, Nielsen J, Siewers V, Shaw AJ. Production of 10-methyl branched fatty acids in yeast. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:12. [PMID: 33413611 PMCID: PMC7791843 DOI: 10.1186/s13068-020-01863-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Despite the environmental value of biobased lubricants, they account for less than 2% of global lubricant use due to poor thermo-oxidative stability arising from the presence of unsaturated double bonds. Methyl branched fatty acids (BFAs), particularly those with branching near the acyl-chain mid-point, are a high-performance alternative to existing vegetable oils because of their low melting temperature and full saturation. RESULTS We cloned and characterized two pathways to produce 10-methyl BFAs isolated from actinomycetes and γ-proteobacteria. In the two-step bfa pathway of actinomycetes, BfaB methylates Δ9 unsaturated fatty acids to form 10-methylene BFAs, and subsequently, BfaA reduces the double bond to produce a fully saturated 10-methyl branched fatty acid. A BfaA-B fusion enzyme increased the conversion efficiency of 10-methyl BFAs. The ten-methyl palmitate production (tmp) pathway of γ-proteobacteria produces a 10-methylene intermediate, but the TmpA putative reductase was not active in E. coli or yeast. Comparison of BfaB and TmpB activities revealed a range of substrate specificities from C14-C20 fatty acids unsaturated at the Δ9, Δ10 or Δ11 position. We demonstrated efficient production of 10-methylene and 10-methyl BFAs in S. cerevisiae by secretion of free fatty acids and in Y. lipolytica as triacylglycerides, which accumulated to levels more than 35% of total cellular fatty acids. CONCLUSIONS We report here the characterization of a set of enzymes that can produce position-specific methylene and methyl branched fatty acids. Yeast expression of bfa enzymes can provide a platform for the large-scale production of branched fatty acids suitable for industrial and consumer applications.
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Affiliation(s)
- Hannah G Blitzblau
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA.
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA.
| | - Andrew L Consiglio
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA
| | - Paulo Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
| | | | - Shuyan Chen
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA
| | - Oliver Konzock
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Gamuchirai Chifamba
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA
| | - Austin Su
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
| | - Annapurna Kamineni
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA
| | - Kyle MacEwen
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA
| | - Maureen Hamilton
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA
| | - Vasiliki Tsakraklides
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Ginkgo BioWorks, 27 Drydock Ave., Boston, MA, 02210, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, 2200, Copenhagen N, Denmark
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
| | - A Joe Shaw
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
- Manus Biosynthesis, 1030 Massachusetts Ave. #300, Cambridge, MA, 02138, USA
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Cambier CJ, Banik SM, Buonomo JA, Bertozzi CR. Spreading of a mycobacterial cell-surface lipid into host epithelial membranes promotes infectivity. eLife 2020; 9:60648. [PMID: 33226343 PMCID: PMC7735756 DOI: 10.7554/elife.60648] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/23/2020] [Indexed: 12/31/2022] Open
Abstract
Several virulence lipids populate the outer cell wall of pathogenic mycobacteria. Phthiocerol dimycocerosate (PDIM), one of the most abundant outer membrane lipids, plays important roles in both defending against host antimicrobial programs and in evading these programs altogether. Immediately following infection, mycobacteria rely on PDIM to evade Myd88-dependent recruitment of microbicidal monocytes which can clear infection. To circumvent the limitations in using genetics to understand virulence lipids, we developed a chemical approach to track PDIM during Mycobacterium marinum infection of zebrafish. We found that PDIM's methyl-branched lipid tails enabled it to spread into host epithelial membranes to prevent immune activation. Additionally, PDIM’s affinity for cholesterol promoted this phenotype; treatment of zebrafish with statins, cholesterol synthesis inhibitors, decreased spreading and provided protection from infection. This work establishes that interactions between host and pathogen lipids influence mycobacterial infectivity and suggests the use of statins as tuberculosis preventive therapy by inhibiting PDIM spread.
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Affiliation(s)
- C J Cambier
- Department of Chemistry, Stanford University, Stanford, United States
| | - Steven M Banik
- Department of Chemistry, Stanford University, Stanford, United States
| | - Joseph A Buonomo
- Department of Chemistry, Stanford University, Stanford, United States
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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23
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Song HS, Choi TR, Bhatia SK, Lee SM, Park SL, Lee HS, Kim YG, Kim JS, Kim W, Yang YH. Combination Therapy Using Low-Concentration Oxacillin with Palmitic Acid and Span85 to Control Clinical Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2020; 9:antibiotics9100682. [PMID: 33049970 PMCID: PMC7599641 DOI: 10.3390/antibiotics9100682] [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: 08/27/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 11/16/2022] Open
Abstract
The overuse of antibiotics has led to the emergence of multidrug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA). MRSA is difficult to kill with a single antibiotic because it has evolved to be resistant to various antibiotics by increasing the PBP2a (mecA) expression level, building up biofilm, introducing SCCmec for multidrug resistance, and changing its membrane properties. Therefore, to overcome antibiotic resistance and decrease possible genetic mutations that can lead to the acquisition of higher antibiotic resistance, drug combination therapy was applied based on previous results indicating that MRSA shows increased susceptibility to free fatty acids and surfactants. The optimal ratio of three components and the synergistic effects of possible combinations were investigated. The combinations were directly applied to clinically isolated strains, and the combination containing 15 μg/mL of oxacillin was able to control SCCmec type III and IV isolates having an oxacillin minimum inhibitory concentration (MIC) up to 1024 μg/mL; moreover, the combination with a slightly increased oxacillin concentration was able to kill SCCmec type II. Phospholipid analysis revealed that clinical strains with higher resistance contained a high portion of 12-methyltetradecanoic acid (anteiso-C15:0) and 14-methylhexadecanoic acid (anteiso-C17:0), although individual strains showed different patterns. In summary, we showed that combinatorial therapy with a low concentration of oxacillin controlled different laboratory and highly diversified clinical MRSA strains.
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Affiliation(s)
- Hun-Suk Song
- Department of Biological Engineering, College of Engineering, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea; (H.-S.S.); (T.-R.C.); (S.K.B.); (S.M.L.); (S.L.P.); (H.S.L.)
| | - Tae-Rim Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea; (H.-S.S.); (T.-R.C.); (S.K.B.); (S.M.L.); (S.L.P.); (H.S.L.)
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea; (H.-S.S.); (T.-R.C.); (S.K.B.); (S.M.L.); (S.L.P.); (H.S.L.)
- Institute for Ubiquitous Information Technology and Applications (CBRU), Konkuk University, Seoul 05029, Korea
| | - Sun Mi Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea; (H.-S.S.); (T.-R.C.); (S.K.B.); (S.M.L.); (S.L.P.); (H.S.L.)
| | - Sol Lee Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea; (H.-S.S.); (T.-R.C.); (S.K.B.); (S.M.L.); (S.L.P.); (H.S.L.)
| | - Hye Soo Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea; (H.-S.S.); (T.-R.C.); (S.K.B.); (S.M.L.); (S.L.P.); (H.S.L.)
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, 511 Sangdo-dong, Seoul 156-743, Korea;
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea;
| | - Wooseong Kim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea;
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea; (H.-S.S.); (T.-R.C.); (S.K.B.); (S.M.L.); (S.L.P.); (H.S.L.)
- Institute for Ubiquitous Information Technology and Applications (CBRU), Konkuk University, Seoul 05029, Korea
- Correspondence:
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de Carvalho CCCR, Teixeira R, Fernandes P. Mycobacterium vaccae Adaptation to Disinfectants and Hand Sanitisers, and Evaluation of Cross-Tolerance with Antimicrobials. Antibiotics (Basel) 2020; 9:antibiotics9090544. [PMID: 32867093 PMCID: PMC7559525 DOI: 10.3390/antibiotics9090544] [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] [Received: 08/04/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium vaccae is being considered as an adjuvant to antituberculosis therapy, tested for the treatment of autoimmune diseases, and as an anti-depressive agent. This bacterium is ubiquitous in the environment and the widespread use of disinfectants and sanitisers may lead to its adaptation to these compounds. In the present study, M. vaccae cells adapted to these compounds mainly by making adjustments in their lipid composition and net surface charge. The modifications in the lipid composition led to changes in membrane permeability which resulted in increased tolerance towards levofloxacin, thioridazine, and omeprazole.
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Affiliation(s)
- Carla C. C. R. de Carvalho
- Department of Bioengineering, iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (R.T.); (P.F.)
- Correspondence: ; Tel.: +351-21-841-9594
| | - Raquel Teixeira
- Department of Bioengineering, iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (R.T.); (P.F.)
| | - Pedro Fernandes
- Department of Bioengineering, iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (R.T.); (P.F.)
- DREAMS and Faculty of Engineering, Universidade Lusófona de Humanidades e Tecnologias, 1749-024 Lisbon, Portugal
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25
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Loschwitz J, Olubiyi OO, Hub JS, Strodel B, Poojari CS. Computer simulations of protein-membrane systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:273-403. [PMID: 32145948 PMCID: PMC7109768 DOI: 10.1016/bs.pmbts.2020.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Olujide O Olubiyi
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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26
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Sharma AR, Harunari E, Zhou T, Trianto A, Igarashi Y. Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp. Beilstein J Org Chem 2019; 15:2327-2332. [PMID: 31666867 PMCID: PMC6808205 DOI: 10.3762/bjoc.15.225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/16/2019] [Indexed: 12/22/2022] Open
Abstract
(2Z,4E)-3-Methyl-2,4-decadienoic acid (1) was identified as a major metabolite from a culture extract of a marine bacterium Microbulbifer which was collected from a stony coral Porites sp. NMR-based spectroscopic analysis revealed that 1 is an unsaturated fatty acid in which a methyl group is located in an uncommon position as a natural product. Feeding experiments of 13C-labeled precursors clarified that ʟ-methionine-derived methylation takes place at the carbon which is derived from the carbonyl carbon of acetate. Compound 1 showed weak growth inhibition against Saccharomyces cerevisiae.
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Affiliation(s)
- Amit Raj Sharma
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Agus Trianto
- Faculty of Fisheries and Marine Sciences, Diponegoro University, Tembalang Campus, St. Prof. Soedarto SH., Semarang 50275, Central Java, Indonesia
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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27
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Dairy Fat Consumption and the Risk of Metabolic Syndrome: An Examination of the Saturated Fatty Acids in Dairy. Nutrients 2019; 11:nu11092200. [PMID: 31547352 PMCID: PMC6769731 DOI: 10.3390/nu11092200] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023] Open
Abstract
Lifestyle is a key modifiable risk factor involved in the manifestation of metabolic syndrome and, in particular, diet plays a pivotal role in its prevention and development. Current dietary guidelines discourage the consumption of saturated fat and dietary sources rich in saturated fat, such as dairy products, despite data suggesting that full-fat dairy consumption is protective against metabolic syndrome. This narrative review assessed the recent epidemiological and clinical research that examined the consumption of dairy-derived saturated fatty acids (SFA) on metabolic syndrome risk. In addition, this review evaluated studies of individual SFA to gain insight into the potential mechanisms at play with intake of a diet enriched with these dairy-derived fatty acids. This work underscores that SFA are a heterogenous class of fatty acids that can differ considerably in their biological activity within the body depending on their length and specific chemical structure. In summary, previous work on the impact of dairy-derived SFA consumption on disease risk suggests that there is currently insufficient evidence to support current dietary guidelines which consolidate all dietary SFA into a single group of nutrients whose consumption should be reduced, regardless of dietary source, food matrix, and composition.
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28
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The synthesis of branched-chain fatty acids is limited by enzymatic decarboxylation of ethyl- and methylmalonyl-CoA. Biochem J 2019; 476:2427-2447. [PMID: 31416829 PMCID: PMC6717113 DOI: 10.1042/bcj20190500] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022]
Abstract
Most fatty acids (FAs) are straight chains and are synthesized by fatty acid synthase (FASN) using acetyl-CoA and malonyl-CoA units. Yet, FASN is known to be promiscuous as it may use methylmalonyl-CoA instead of malonyl-CoA and thereby introduce methyl-branches. We have recently found that the cytosolic enzyme ECHDC1 degrades ethylmalonyl-CoA and methylmalonyl-CoA, which presumably result from promiscuous reactions catalyzed by acetyl-CoA carboxylase on butyryl- and propionyl-CoA. Here, we tested the hypothesis that ECHDC1 is a metabolite repair enzyme that serves to prevent the formation of methyl- or ethyl-branched FAs by FASN. Using the purified enzyme, we found that FASN can incorporate not only methylmalonyl-CoA but also ethylmalonyl-CoA, producing methyl- or ethyl-branched FAs. Using a combination of gas-chromatography and liquid chromatography coupled to mass spectrometry, we observed that inactivation of ECHDC1 in adipocytes led to an increase in several methyl-branched FAs (present in different lipid classes), while its overexpression reduced them below wild-type levels. In contrast, the formation of ethyl-branched FAs was observed almost exclusively in ECHDC1 knockout cells, indicating that ECHDC1 and the low activity of FASN toward ethylmalonyl-CoA efficiently prevent their formation. We conclude that ECHDC1 performs a typical metabolite repair function by destroying methyl- and ethylmalonyl-CoA. This reduces the formation of methyl-branched FAs and prevents the formation of ethyl-branched FAs by FASN. The identification of ECHDC1 as a key modulator of the abundance of methyl-branched FAs opens the way to investigate their function.
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29
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Rózsa ZB, Németh LJ, Jójárt B, Nehéz K, Viskolcz B, Szőri M. Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models. J Phys Chem B 2019; 123:7869-7884. [DOI: 10.1021/acs.jpcb.9b04313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Zsófia Borbála Rózsa
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Lukács József Németh
- Department of Food Engineering, Faculty of Engineering, University of Szeged, Mars tér 7, 6724 Szeged, Hungary
| | - Balázs Jójárt
- Department of Food Engineering, Faculty of Engineering, University of Szeged, Mars tér 7, 6724 Szeged, Hungary
| | - Károly Nehéz
- Department of Information Engineering, University of Miskolc, Miskolc-Egyetemváros Informatics Building, H-3515 Miskolc, Hungary
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
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30
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Bouraoui A, Ghanem R, Berchel M, Vié V, Le Guen Y, Paboeuf G, Deschamps L, Le Gall T, Montier T, Jaffrès PA. Bis-Thioether-Containing Lipid Chains in Cationic Amphiphiles: Physicochemical Properties and Applications in Gene Delivery. Chemphyschem 2019; 20:2187-2194. [PMID: 31393059 DOI: 10.1002/cphc.201900626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/18/2019] [Indexed: 11/08/2022]
Abstract
Cationic amphiphiles featuring two thioether functions in each lipid chain of bicatenar cationic amphiphiles are reported here for the first time. The physicochemical properties and transfection abilities of these new amphiphiles were compared with those of already reported analogues featuring either (i) saturated, (ii) unsaturated or (iii) mono-thioether containing lipid chains. The homogeneity of the series of new compounds allowed to clearly underscore the effect of bis-thioether containing lipid chains. This study shows that besides previous strategies based on unsaturation or ramification, the incorporation of two thioether functions per lipid chain constitutes an original complementary alternative to tune the supramolecular properties of amphiphilic compounds. The potential of this strategy was evaluated in the context of gene delivery and report that two cationic amphiphiles (i. e. 4 a and 4 b) can be proposed as new efficient transfection reagents.
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Affiliation(s)
- Amal Bouraoui
- Univ Brest, CNRS, CEMCA, UMR CNRS 6521, 6 Avenue Victor Le Gorgeu, F-29238, Brest, France
| | - Rosy Ghanem
- Univ Brest, INSERM UMR 1078, IBSAM, UFR Médecine et Sciences de la Santé, CHRU Brest, 22 avenue Camille Desmoulins, F-29238, Brest, France
| | - Mathieu Berchel
- Univ Brest, CNRS, CEMCA, UMR CNRS 6521, 6 Avenue Victor Le Gorgeu, F-29238, Brest, France
| | - Véronique Vié
- Univ Rennes, CNRS, IPR - UMR 6251, ScanMAT - UMS 2001, F-35000, Rennes, France
| | - Yann Le Guen
- Univ Brest, INSERM UMR 1078, IBSAM, UFR Médecine et Sciences de la Santé, CHRU Brest, 22 avenue Camille Desmoulins, F-29238, Brest, France
| | - Gilles Paboeuf
- Univ Rennes, CNRS, IPR - UMR 6251, ScanMAT - UMS 2001, F-35000, Rennes, France
| | - Laure Deschamps
- Univ Brest, CNRS, CEMCA, UMR CNRS 6521, 6 Avenue Victor Le Gorgeu, F-29238, Brest, France
| | - Tony Le Gall
- Univ Brest, INSERM UMR 1078, IBSAM, UFR Médecine et Sciences de la Santé, CHRU Brest, 22 avenue Camille Desmoulins, F-29238, Brest, France
| | - Tristan Montier
- Univ Brest, INSERM UMR 1078, IBSAM, UFR Médecine et Sciences de la Santé, CHRU Brest, 22 avenue Camille Desmoulins, F-29238, Brest, France
| | - Paul-Alain Jaffrès
- Univ Brest, CNRS, CEMCA, UMR CNRS 6521, 6 Avenue Victor Le Gorgeu, F-29238, Brest, France
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31
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Abstract
Triclosan and chloroxylenol are broad-spectrum biocides used extensively in healthcare and consumer products. They have been suggested to perturb the structure of bacterial membranes, but studies so far have not considered that most bacterial membranes contain large amounts of branched-chain lipids. Here, molecular dynamics simulation is used to examine the effect of the two biocides on membranes consisting of lipids with methyl-branched chains, cyclopropanated chains, and nonbranched chains. It is shown that triclosan and chloroxylenol induced a phase transition in membranes from a liquid-crystalline to a liquid-ordered phase irrespective of the presence and nature of branching groups. At high concentration, chloroxylenol promoted chain interdigitation. Our results suggest that triclosan and chloroxylenol decrease the degree of fluidity of membranes and that this effect is more pronounced in bacterial membranes. As a result, their biocidal activity could be associated with a change in the function of membrane proteins.
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Affiliation(s)
- David Poger
- School of Chemistry & Molecular Biosciences , The University of Queensland , Brisbane QLD 4072 , Australia
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences , The University of Queensland , Brisbane QLD 4072 , Australia
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32
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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Engineering microbial membranes to increase stress tolerance of industrial strains. Metab Eng 2019; 53:24-34. [DOI: 10.1016/j.ymben.2018.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/29/2018] [Accepted: 12/29/2018] [Indexed: 12/29/2022]
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Akondi RN, Sharma S, Trexler RV, Mouser PJ, Pfiffner SM. Microbial lipid biomarkers detected in deep subsurface black shales. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:291-307. [PMID: 30688342 DOI: 10.1039/c8em00444g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Evidence for microbes has been detected in extreme subsurface environments as deep as 2.5 km with temperatures as high as 90 °C, demonstrating that microbes can adapt and survive extreme environmental conditions. Deep subsurface shales are increasingly exploited for their energy applications, thus characterizing the prevalence and role of microbes in these ecosystems essential for understanding biogeochemical cycles and maximizing production from hydrocarbon-bearing formations. Here, we describe the distribution of bacterial ester-linked phospholipid fatty acids (PLFA) and diglyceride fatty acids (DGFA) in sidewall cores retrieved from three distinct geologic horizons collected to 2275 m below ground surface in a Marcellus Shale well, West Virginia, USA. We examined the abundance and variety of PLFA and DGFA prior to energy development within and above the Marcellus Shale Formation into the overlying Mahantango Formation of the Appalachian Basin. Lipid biomarkers in the cores suggest the presence of microbial communities comprising Gram (+), Gram (-) as well as stress indicative biomarkers. Microbial PLFA and DGFA degradation in the subsurface can be influenced by stressful environmental conditions associated with the subsurface. The PLFA concentration and variety were higher in the transition zone between the extremely low permeability Marcellus Shale Formation and the more permeable Mahantango Formation. In contrast to this distribution, more abundant and diverse DGFA membrane profiles were associated with the Mahantango Formation. The stress indicative biomarkers like the trans-membrane fatty acids, oxiranes, keto-, and dimethyl lipid fatty acids were present in all cores, potentially indicating that the bacterial communities had experienced physiological stress or nutrient deprivation during or after deposition. The DGFA profiles expressed more stress indicative biomarkers as opposed to the PLFA membrane profiles. These findings suggest the probable presence of indigenous microbial communities in the deep subsurface shale and also improves our understanding of microbial survival mechanisms in ancient deep subsurface environments.
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Affiliation(s)
- Rawlings N Akondi
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506, USA.
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Perez-Lopez MI, Mendez-Reina R, Trier S, Herrfurth C, Feussner I, Bernal A, Forero-Shelton M, Leidy C. Variations in carotenoid content and acyl chain composition in exponential, stationary and biofilm states of Staphylococcus aureus, and their influence on membrane biophysical properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:978-987. [PMID: 30771288 DOI: 10.1016/j.bbamem.2019.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 01/01/2023]
Abstract
Bacteria are often found in close association with surfaces, resulting in the formation of biofilms. In Staphylococcus aureus (S. aureus), biofilms are implicated in the resilience of chronic infections, presenting a serious clinical problem world-wide. Here, S. aureus biofilms are grown under flow within clinical catheters at 37 °C. The lipid composition and biophysical properties of lipid extracts from these biofilms are compared with those from exponential growth and stationary phase cells. Biofilms show a reduction in iso and anteiso branching compensated by an increase in saturated fatty acids compared to stationary phase. A drastic reduction in carotenoid levels is also observed during biofilm formation. Thermotropic measurements of Laurdan GP and DPH polarization, show a reduction of lipid packing at 37 °C for biofilms compared to stationary phase. We studied the effects of carotenoid content on DMPG and DPPG model membranes showing trends in thermotropic behavior consistent with those observed in bacterial isolates, indicating that carotenoids participate in modulating lipid packing. Additionally, bending elastic constant (kc) measurements using vesicle fluctuation analysis (VFA) show that the presence of carotenoids can increase membrane bending rigidity. The antimicrobial peptide Magainin H2 was less activity on liposomes composed of stationary phase compared to biofilms or exponential growth isolates. This study contributes to an understanding of how Staphylococcus aureus modulates the composition of its membrane lipids, and how those changes affect the biophysical properties of membranes, which in turn may play a role in its virulence and its resistance to different membrane-active antimicrobial agents.
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Affiliation(s)
- Maria Isabel Perez-Lopez
- Department of Physics, Universidad de los Andes, Bogotá, Colombia; Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | | | - Steve Trier
- Department of Physics, Universidad de los Andes, Bogotá, Colombia
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany; Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Adriana Bernal
- Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
| | | | - Chad Leidy
- Department of Physics, Universidad de los Andes, Bogotá, Colombia.
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Bai W, Geng W, Wang S, Zhang F. Biosynthesis, regulation, and engineering of microbially produced branched biofuels. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:84. [PMID: 31011367 PMCID: PMC6461809 DOI: 10.1186/s13068-019-1424-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/03/2019] [Indexed: 05/13/2023]
Abstract
The steadily increasing demand on transportation fuels calls for renewable fuel replacements. This has attracted a growing amount of research to develop advanced biofuels that have similar physical, chemical, and combustion properties with petroleum-derived fossil fuels. Early generations of biofuels, such as ethanol, butanol, and straight-chain fatty acid-derived esters or hydrocarbons suffer from various undesirable properties and can only be blended in limited amounts. Recent research has shifted to the production of branched-chain biofuels that, compared to straight-chain fuels, have higher octane values, better cold flow, and lower cloud points, making them more suitable for existing engines, particularly for diesel and jet engines. This review focuses on several types of branched-chain biofuels and their immediate precursors, including branched short-chain (C4-C8) and long-chain (C15-C19)-alcohols, alkanes, and esters. We discuss their biosynthesis, regulation, and recent efforts in their overproduction by engineered microbes.
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Affiliation(s)
- Wenqin Bai
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Weitao Geng
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Shaojie Wang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130 USA
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, MO 63130 USA
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de Carvalho CCCR, Caramujo MJ. The Various Roles of Fatty Acids. Molecules 2018; 23:molecules23102583. [PMID: 30304860 PMCID: PMC6222795 DOI: 10.3390/molecules23102583] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/01/2018] [Accepted: 10/06/2018] [Indexed: 12/31/2022] Open
Abstract
Lipids comprise a large group of chemically heterogeneous compounds. The majority have fatty acids (FA) as part of their structure, making these compounds suitable tools to examine processes raging from cellular to macroscopic levels of organization. Among the multiple roles of FA, they have structural functions as constituents of phospholipids which are the "building blocks" of cell membranes; as part of neutral lipids FA serve as storage materials in cells; and FA derivatives are involved in cell signalling. Studies on FA and their metabolism are important in numerous research fields, including biology, bacteriology, ecology, human nutrition and health. Specific FA and their ratios in cellular membranes may be used as biomarkers to enable the identification of organisms, to study adaptation of bacterial cells to toxic compounds and environmental conditions and to disclose food web connections. In this review, we discuss the various roles of FA in prokaryotes and eukaryotes and highlight the application of FA analysis to elucidate ecological mechanisms. We briefly describe FA synthesis; analyse the role of FA as modulators of cell membrane properties and FA ability to store and supply energy to cells; and inspect the role of polyunsaturated FA (PUFA) and the suitability of using FA as biomarkers of organisms.
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Affiliation(s)
- Carla C C R de Carvalho
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Maria José Caramujo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2-5º Piso, 1749-016 Lisboa, Portugal.
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Cho BC, Hardies SC, Jang GI, Hwang CY. Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6 T adapted to coastal planktonic lifestyle. BMC Genomics 2018; 19:625. [PMID: 30134835 PMCID: PMC6106888 DOI: 10.1186/s12864-018-5019-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/14/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Pontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environment in which members of Microbactericeae have not been previously characterized. RESULTS The genome of P. salivibrio CL-TW6T was a single chromosome of 1,760,810 bp. Genomes of this small size are typically found in bacteria growing slowly in oligotrophic zones and said to be streamlined. Phylogenetic analysis showed it to represent a lineage originating in the Microbacteriaceae radiation occurring before the snowball Earth glaciations, and to have a closer relationship with some streamlined bacteria known through metagenomic data. Several genomic characteristics typical of streamlined bacteria are found: %G + C is lower than non-streamlined members of the phylum; there are a minimal number of rRNA and tRNA genes, fewer paralogs in most gene families, and only two sigma factors; there is a noticeable absence of some nonessential metabolic pathways, including polyketide synthesis and catabolism of some amino acids. There was no indication of any phage genes or plasmids, however, a system of active insertion elements was present. P. salivibrio appears to be unusual in having polyrhamnose-based cell wall oligosaccharides instead of mycolic acid or teichoic acid-based oligosaccharides. Oddly, it conducts sulfate assimilation apparently for sulfating cell wall components, but not for synthesizing amino acids. One gene family it has more of, rather than fewer of, are toxin/antitoxin systems, which are thought to down-regulate growth during nutrient deprivation or other stressful conditions. CONCLUSIONS Because of the relatively small number of paralogs and its relationship to the heavily characterized Mycobacterium tuberculosis, we were able to heavily annotate the genome of P. salivibrio CL-TW6T. Its streamlined status and relationship to streamlined metagenomic constructs makes it an important reference genome for study of the streamlining concept. The final evolutionary trajectory of CL-TW6 T was to adapt to growth in a non-oligotrophic coastal zone. To understand that adaptive process, we give a thorough accounting of gene content, contrasting with both oligotrophic streamlined bacteria and large genome bacteria, and distinguishing between genes derived by vertical and horizontal descent.
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Affiliation(s)
- Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Stephen C. Hardies
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Chung Yeon Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
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Pacífico C, Fernandes P, de Carvalho CCCR. Mycobacterial Response to Organic Solvents and Possible Implications on Cross-Resistance With Antimicrobial Agents. Front Microbiol 2018; 9:961. [PMID: 29867865 PMCID: PMC5962743 DOI: 10.3389/fmicb.2018.00961] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/24/2018] [Indexed: 02/02/2023] Open
Abstract
Mycobacterium vaccae, a bacterium found in soil, has been receiving attention as adjuvant to antituberculosis treatment, vaccines and immunotherapies and even as antidepressant. This bacterium is also able to degrade several pollutants, including aromatic compounds. The increasing presence of organic solvents in the environment may lead to M. vaccae adapted populations. A possible relationship between solvent tolerance and decreased susceptibility to other types of chemicals, including antibiotics, may pose a problem during opportunistic infections. The present study thus aimed at assessing if solvent adapted cells presented higher tolerance to antibiotics and efflux pump inhibitors (EPIs). M. vaccae cells were able to thrive and grow in the presence of up 20% (v/v) glycerol, 5% (v/v) ethanol, 1% (v/v) methyl tert-butyl ether (MTBE) and 0.1% (v/v) toluene. During adaptation to increasing concentration of ethanol and MTBE, the cells changed their fatty acid profile, zeta potential and morphology. Adapted cells acquired an improved tolerance toward the EPIs thioridazine and omeprazole, but became more susceptible to the antibiotics levofloxacin and teicoplanin when compared with non-adapted cells.
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Affiliation(s)
- Cátia Pacífico
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro Fernandes
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Faculty of Engineering, Universidade Lusófona, Lisbon, Portugal
| | - Carla C. C. R. de Carvalho
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Singh VK, Sirobhushanam S, Ring RP, Singh S, Gatto C, Wilkinson BJ. Roles of pyruvate dehydrogenase and branched-chain α-keto acid dehydrogenase in branched-chain membrane fatty acid levels and associated functions in Staphylococcus aureus. J Med Microbiol 2018; 67:570-578. [PMID: 29498620 PMCID: PMC5982145 DOI: 10.1099/jmm.0.000707] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/15/2018] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Membrane fluidity to a large extent is governed by the presence of branched-chain fatty acids (BCFAs). Branched-chain α-keto acid dehydrogenase (BKD) is the key enzyme in BCFA synthesis. A Staphylococcus aureus BKD-deficient strain still produced substantial levels of BCFAs. Pyruvate dehydrogenase (PDH) with structural similarity to BKD has been speculated to contribute to BCFAs in S. aureus. METHODOLOGY This study was carried out using BKD-, PDH- and BKD : PDH-deficient derivatives of methicillin-resistant S. aureus strain JE2. Differences in growth kinetics were evaluated spectrophotometrically, membrane BCFAs using gas chromatography and membrane fluidity by fluorescence polarization. Carotenoid levels were estimated by measuring A465 of methanol extracts from 48 h cultures. MIC values were determined by broth microdilution.Results/Key findings. BCFAs made up 50 % of membrane fatty acids in wild-type but only 31 % in the BKD-deficient mutant. BCFA level was ~80 % in the PDH-deficient strain and 38 % in the BKD : PDH-deficient strain. BKD-deficient mutant showed decreased membrane fluidity, the PDH-deficient mutant showed increased membrane fluidity. The BKD- and PDH-deficient strains grew slower and the BKD : PDH-deficient strain grew slowest at 37 °C. However at 20 °C, the BKD- and BKD : PDH-deficient strains grew only a little followed by autolysis of these cells. The BKD-deficient strain produced higher levels of staphyloxanthin. The PDH-deficient and BKD : PDH-deficient strains produced very little staphyloxanthin. The BKD-deficient strain showed increased susceptibility to daptomycin. CONCLUSION The BCFA composition of the cell membrane in S. aureus seems to significantly impact cell growth, membrane fluidity and resistance to daptomycin.
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Affiliation(s)
- Vineet K. Singh
- Microbiology & Immunology, A.T. Still University of Health Sciences, Kirksville, MO 63501, USA
| | - Sirisha Sirobhushanam
- Microbiology Group, School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Robert P. Ring
- Microbiology & Immunology, A.T. Still University of Health Sciences, Kirksville, MO 63501, USA
| | - Saumya Singh
- Microbiology & Immunology, A.T. Still University of Health Sciences, Kirksville, MO 63501, USA
| | - Craig Gatto
- Microbiology Group, School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Brian J. Wilkinson
- Microbiology Group, School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
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42
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Nuez-Ortín WG, Carter CG, Nichols PD, Cooke IR, Wilson R. Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature. BMC Genomics 2018; 19:133. [PMID: 29433420 PMCID: PMC5809918 DOI: 10.1186/s12864-018-4517-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
Background Atlantic salmon production in Tasmania (Southern Australia) occurs near the upper limits of the species thermal tolerance. Summer water temperatures can average over 19 °C over several weeks and have negative effects on performance and health. Liver tissue exerts important metabolic functions in thermal adaptation. With the aim of identifying mechanisms underlying liver plasticity in response to chronic elevated temperature in Atlantic salmon, label-free shotgun proteomics was used to explore quantitative protein changes after 43 days of exposure to elevated temperature. Results A total of 276 proteins were differentially (adjusted p-value < 0.05) expressed between the control (15 °C) and elevated (21 °C) temperature treatments. As identified by Ingenuity Pathway Analysis (IPA), transcription and translation mechanisms, protein degradation via the proteasome, and cytoskeletal components were down-regulated at elevated temperature. In contrast, an up-regulated response was identified for NRF2-mediated oxidative stress, endoplasmic reticulum stress, and amino acid degradation. The proteome response was paralleled by reduced fish condition factor and hepato-somatic index at elevated temperature. Conclusions The present study provides new evidence of the interplay among different cellular machineries in a scenario of heat-induced energy deficit and oxidative stress, and refines present understanding of how Atlantic salmon cope with chronic exposure to temperature near the upper limits of thermal tolerance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4517-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Waldo G Nuez-Ortín
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS 7001, Australia.
| | - Chris G Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS 7001, Australia
| | - Peter D Nichols
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS 7001, Australia.,CSIRO Food Nutrition and Bio-based Products, Oceans & Atmosphere, GPO Box 1538, Hobart, TAS 7001, Australia
| | - Ira R Cooke
- Comparative Genomics Centre, James Cook University, Townsville, QLD, 4811, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Bag 74, Hobart, TAS 7001, Australia
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Sieniawska E, Sawicki R, Swatko-Ossor M, Napiorkowska A, Przekora A, Ginalska G, Augustynowicz-Kopec E. The Effect of Combining Natural Terpenes and Antituberculous Agents against Reference and Clinical Mycobacterium tuberculosis Strains. Molecules 2018; 23:E176. [PMID: 29342972 PMCID: PMC6017631 DOI: 10.3390/molecules23010176] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/28/2017] [Accepted: 01/06/2018] [Indexed: 11/17/2022] Open
Abstract
Background: On account of emergence of multi- and extensively drug-resistant Mycobacterium tuberculosis (Mtb) strains, combinations of drugs with natural compounds were tested to search for antibiotic activity enhancers. In this work we studied terpenes (α-pinene, bisabolol, β-elemene, (R)-limonene, (S)-limonene, myrcene, sabinene), which are the main constituents of essential oil obtained from Mutellina purpurea L., a plant with described antitubercular activity, to investigate their interactions with antibiotics against reference Mtb strains and multidrug-resistant clinical isolates. Methods: The serial dilution method was used to evaluate the minimal inhibitory concentration (MIC) of tested compounds, while the fractional inhibitory concentration index (FICI) was calculated for characterization of interactions. Moreover, IC50 values of tested compounds were determined using monkey kidney epithelial cell line (GMK). Results: The combinations of all studied terpenes with ethambutol or rifampicin resulted in a synergistic interaction. Bisabolol and (R)-limonene decreased the MIC for rifampicin at least two-fold for all tested strains, however no synergistic action was observed against virulent strains. The tested terpenes showed slight (bisabolol) or no cytotoxic effect against normal eukaryotic cells in vitro. Conclusions: The obtained enhanced activity (FICI < 0.5) of ethambutol and rifampicin against H37Ra strain under the influence of the studied terpenes may be correlated to the capability of essential oil constituents to modify bacterial resistance mechanisms in general. The observed differences in avirulent and virulent bacteria susceptibility to terpenes tested separately and in combinations with antibiotics can be correlated with the differences in the cell wall structure between H37Ra mutant and all virulent strains.
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Affiliation(s)
- Elwira Sieniawska
- Department of Pharmacognosy with Medicinal Plant Unit, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Rafal Sawicki
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Marta Swatko-Ossor
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Agnieszka Napiorkowska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland.
| | - Agata Przekora
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Grazyna Ginalska
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland.
| | - Ewa Augustynowicz-Kopec
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland.
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44
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John T, Thomas T, Abel B, Wood BR, Chalmers DK, Martin LL. How kanamycin A interacts with bacterial and mammalian mimetic membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2242-2252. [DOI: 10.1016/j.bbamem.2017.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/09/2017] [Accepted: 08/23/2017] [Indexed: 01/11/2023]
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45
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Sollich M, Yoshinaga MY, Häusler S, Price RE, Hinrichs KU, Bühring SI. Heat Stress Dictates Microbial Lipid Composition along a Thermal Gradient in Marine Sediments. Front Microbiol 2017; 8:1550. [PMID: 28878741 PMCID: PMC5572230 DOI: 10.3389/fmicb.2017.01550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 07/31/2017] [Indexed: 12/17/2022] Open
Abstract
Temperature exerts a first-order control on microbial populations, which constantly adjust the fluidity and permeability of their cell membrane lipids to minimize loss of energy by ion diffusion across the membrane. Analytical advances in liquid chromatography coupled to mass spectrometry have allowed the detection of a stunning diversity of bacterial and archaeal lipids in extreme environments such as hot springs, hydrothermal vents and deep subsurface marine sediments. Here, we investigated a thermal gradient from 18 to 101°C across a marine sediment field and tested the hypothesis that cell membrane lipids provide a major biochemical basis for the bioenergetics of archaea and bacteria under heat stress. This paper features a detailed lipidomics approach with the focus on membrane lipid structure-function. Membrane lipids analyzed here include polar lipids of bacteria and polar and core lipids of archaea. Reflecting the low permeability of their ether-linked isoprenoids, we found that archaeal polar lipids generally dominate over bacterial lipids in deep layers of the sediments influenced by hydrothermal fluids. A close examination of archaeal and bacterial lipids revealed a membrane quandary: not only low permeability, but also increased fluidity of membranes are required as a unified property of microbial membranes for energy conservation under heat stress. For instance, bacterial fatty acids were composed of longer chain lengths in concert with higher degree of unsaturation while archaea modified their tetraethers by incorporation of additional methyl groups at elevated sediment temperatures. It is possible that these configurations toward a more fluidized membrane at elevated temperatures are counterbalanced by the high abundance of archaeal glycolipids and bacterial sphingolipids, which could reduce membrane permeability through strong intermolecular hydrogen bonding. Our results provide a new angle for interpreting membrane lipid structure-function enabling archaea and bacteria to survive and grow in hydrothermal systems.
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Affiliation(s)
- Miriam Sollich
- University of Bremen, MARUM Center for Marine Environmental SciencesBremen, Germany
| | - Marcos Y Yoshinaga
- University of Bremen, MARUM Center for Marine Environmental SciencesBremen, Germany.,Institute of Chemistry, University of São PauloSão Paulo, Brazil
| | - Stefan Häusler
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Roy E Price
- University of Bremen, MARUM Center for Marine Environmental SciencesBremen, Germany.,School of Marine and Atmospheric Sciences, Stony Brook University, Stony BrookNY, United States
| | - Kai-Uwe Hinrichs
- University of Bremen, MARUM Center for Marine Environmental SciencesBremen, Germany
| | - Solveig I Bühring
- University of Bremen, MARUM Center for Marine Environmental SciencesBremen, Germany
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Vinçon-Laugier A, Cravo-Laureau C, Mitteau I, Grossi V. Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria. Front Microbiol 2017; 8:1532. [PMID: 28848536 PMCID: PMC5552659 DOI: 10.3389/fmicb.2017.01532] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/28/2017] [Indexed: 11/13/2022] Open
Abstract
The occurrence of non-isoprenoid alkyl glycerol ether lipids in Bacteria and natural environments is increasingly being reported and the specificity and diagenetic stability of these lipids make them powerful biomarkers for biogeochemical and environmental studies. Yet the environmental controls on the biosynthesis of these peculiar membrane lipids remain poorly documented. Here, the lipid content of two mesophilic (Desulfatibacillum aliphaticivorans and Desulfatibacillum alkenivorans) and one thermophilic (Thermodesulfobacterium commune) sulfate-reducing bacteria-whose membranes are mostly composed of ether lipids-was investigated as a function of growth temperature (20-40°C and 54-84°C, respectively). For all strains, the cellular lipid content was lower at sub- or supra-optimal growth temperature, but the relative proportions of dialkyl glycerols, monoalkyl glycerols and fatty acids remained remarkably stable whatever the growth temperature. Rather than changing the proportions of the different lipid classes, the three strains responded to temperature changes by modifying the average structural composition of the alkyl and acyl chains constitutive of their membrane lipids. Major adaptive mechanisms concerned modifications of the level of branching and of the proportions of the different methyl branched lipids. Specifically, an increase in temperature induced mesophilic strains to produce less dimethyl branched dialkyl glycerols and 10-methyl branched lipids relative to linear structures, and the thermophilic strain to decrease the proportion of anteiso relative to iso methyl branched compounds. These modifications were in agreement with a regulation of the membrane fluidity. In one mesophilic and the thermophilic strains, a modification of the growth temperature further induced changes in the relative proportions of sn-2 vs sn-1 monoalkyl glycerols, suggesting an unprecedented mechanism of homeoviscous adaptation in Bacteria. Strong linear correlations observed between different ratios of alkyl glycerols and temperature allow to hypothesize the use of these specific lipids as indicators of temperature changes in the environment.
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Affiliation(s)
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les MatériauxPau, France
| | - Isabelle Mitteau
- Equipe Environnement et Microbiologie, UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les MatériauxPau, France
| | - Vincent Grossi
- Laboratoire de Géologie de Lyon, UMR CNRS 5276, Université Lyon 1Villeurbanne, France
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47
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Kara S, Afonin S, Babii O, Tkachenko AN, Komarov IV, Ulrich AS. Diphytanoyl lipids as model systems for studying membrane-active peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1828-1837. [PMID: 28587828 DOI: 10.1016/j.bbamem.2017.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 01/28/2023]
Abstract
The branched chains in diphytanoyl lipids provide membranes with unique properties, such as high chemical/physical stability, low water permeability, and no gel-to-fluid phase transition at ambient temperature. Synthetic diphytanoyl phospholipids are often used as model membranes for electrophysiological experiments. To evaluate whether these sturdy lipids are also suitable for solid-state NMR, we have examined their interactions with a typical amphiphilic peptide in comparison with straight-chain lipids. First, their phase properties were monitored using 31P NMR, and the structural behaviour of the antimicrobial peptide PGLa was studied by 19F NMR and circular dichroism in oriented membrane samples. Only lipids with choline headgroups (DPhPC) were found to form stable lipid bilayers in oriented samples, while DPhPG, DPhPE and DPhPS display non-lamellar structures. Hence, the experimental temperature and hydration are crucial factors when using supported diphytanoyl lipids, as both parameters must be maintained in an appropriate range to avoid the formation of non-bilayer structures. For the same reason, a high content of other diphytanoyl lipids besides DPhPC in mixed lipid systems is not favourable. Unlike the situation in straight-chain membranes, we found that the α-helical PGLa was not able to insert into the tightly packed fluid bilayer of DPhPC but remained in a surface-bound state even at very high peptide concentration. This behaviour can be explained by the high cohesivity and the negative spontaneous curvature of the diphytanoyl lipids. These characteristic features must therefore be taken into consideration, both, in electrophysiological studies, and when interpreting the structural behaviour of membrane-active peptides in such lipid environment.
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Affiliation(s)
- Sezgin Kara
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O.B. 3640, 76021 Karlsruhe, Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Institute of Biology and Medicine (IBM), Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601 Kyiv, Ukraine
| | - Anton N Tkachenko
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Institute of Biology and Medicine (IBM), Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601 Kyiv, Ukraine
| | - Igor V Komarov
- Enamine Ltd., vul. Chervonotkatska 78, 02094 Kyiv, Ukraine; Institute of High Technologies (IHT), Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601 Kyiv, Ukraine
| | - Anne S Ulrich
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O.B. 3640, 76021 Karlsruhe, Germany.
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48
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Wang LH, Wang MS, Zeng XA, Xu XM, Brennan CS. Membrane and genomic DNA dual-targeting of citrus flavonoid naringenin against Staphylococcus aureus. Integr Biol (Camb) 2017; 9:820-829. [DOI: 10.1039/c7ib00095b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Naringenin exerts its antibacterial action by disruption of the cytoplasmic membrane and DNA targeting effects inStaphylococcus aureus.
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Affiliation(s)
- Lang-Hong Wang
- School of Food Science and Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Man-Sheng Wang
- School of Food Science and Engineering
- South China University of Technology
- Guangzhou 510641
- China
- Institute of Bast Fiber Crops
| | - Xin-An Zeng
- School of Food Science and Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Xi-Ming Xu
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213000
- China
| | - Charles S. Brennan
- Department of Wine
- Food and Molecular Biosciences
- Lincoln University
- Canterbury
- New Zealand
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49
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Sirobhushanam S, Galva C, Saunders LP, Sen S, Jayaswal R, Wilkinson BJ, Gatto C. Utilization of multiple substrates by butyrate kinase from Listeria monocytogenes. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:283-290. [PMID: 27940001 DOI: 10.1016/j.bbalip.2016.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/20/2016] [Accepted: 12/04/2016] [Indexed: 12/17/2022]
Abstract
Listeria monocytogenes, the causative agent of listeriosis, can build up to dangerous levels in refrigerated foods potentially leading to expensive product recalls. An important aspect of the bacterium's growth at low temperatures is its ability to increase the branched-chain fatty acid anteiso C15:0 content of its membrane at lower growth temperatures, which imparts greater membrane fluidity. Mutants in the branched-chain α-keto dehydrogenase (bkd) complex are deficient in branched-chain fatty acids (BCFAs,) but these can be restored by feeding C4 and C5 branched-chain carboxylic acids (BCCAs). This suggests the presence of an alternate pathway for production of acyl CoA precursors for fatty acid biosynthesis. We hypothesize that the alternate pathway is composed of butyrate kinase (buk) and phosphotransbutyrylase (ptb) encoded in the bkd complex which produce acyl CoA products by their sequential action through the metabolism of carboxylic acids. We determined the steady state kinetics of recombinant His-tagged Buk using 11 different straight-chain and BCCA substrates in the acyl phosphate forming direction. Buk demonstrated highest catalytic efficiency with pentanoate as the substrate. Low product formation observed with acetate (C2) and hexanoate (C6) as the substrates indicates that Buk is not involved in either acetate metabolism or long chain carboxylic acid activation. We were also able to show that Buk catalysis occurs through a ternary complex intermediate. Additionally, Buk demonstrates a strong preference for BCCAs at low temperatures. These results indicate that Buk may be involved in the activation and assimilation of exogenous carboxylic acids for membrane fatty acid biosynthesis.
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Affiliation(s)
- Sirisha Sirobhushanam
- School of Biological Sciences, Illinois State University, Normal, IL 61790, United States
| | - Charitha Galva
- School of Biological Sciences, Illinois State University, Normal, IL 61790, United States
| | - Lauren P Saunders
- School of Biological Sciences, Illinois State University, Normal, IL 61790, United States
| | - Suranjana Sen
- School of Biological Sciences, Illinois State University, Normal, IL 61790, United States
| | - Radheshyam Jayaswal
- School of Biological Sciences, Illinois State University, Normal, IL 61790, United States
| | - Brian J Wilkinson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, United States
| | - Craig Gatto
- School of Biological Sciences, Illinois State University, Normal, IL 61790, United States.
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50
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Saunders LP, Sen S, Wilkinson BJ, Gatto C. Insights into the Mechanism of Homeoviscous Adaptation to Low Temperature in Branched-Chain Fatty Acid-Containing Bacteria through Modeling FabH Kinetics from the Foodborne Pathogen Listeria monocytogenes. Front Microbiol 2016; 7:1386. [PMID: 27656167 PMCID: PMC5013041 DOI: 10.3389/fmicb.2016.01386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/22/2016] [Indexed: 11/13/2022] Open
Abstract
The psychrotolerant foodborne pathogen Listeria monocytogenes withstands the stress of low temperatures and can proliferate in refrigerated food. Bacteria adapt to growth at low temperatures by increasing the production of fatty acids that increase membrane fluidity. The mechanism of homeoviscous increases in unsaturated fatty acid amounts in bacteria that predominantly contain straight-chain fatty acids is relatively well understood. By contrast the analogous mechanism in branched-chain fatty acid-containing bacteria, such as L. monocytogenes, is poorly understood. L. monocytogenes grows at low temperatures by altering its membrane composition to increase membrane fluidity, primarily by decreasing the length of fatty acid chains and increasing the anteiso to iso fatty acid ratio. FabH, the initiator of fatty acid biosynthesis, has been identified as the primary determinant of membrane fatty acid composition, but the extent of this effect has not been quantified. In this study, previously determined FabH steady-state parameters and substrate concentrations were used to calculate expected fatty acid compositions at 30°C and 10°C. FabH substrates 2-methylbutyryl-CoA, isobutyryl-CoA, and isovaleryl-CoA produce the primary fatty acids in L. monocytogenes, i.e., anteiso-odd, iso-even, and iso-odd fatty acids, respectively. In vivo concentrations of CoA derivatives were measured, but not all were resolved completely. In this case, estimates were calculated from overall fatty acid composition and FabH steady-state parameters. These relative substrate concentrations were used to calculate the expected fatty acid compositions at 10°C. Our model predicted a higher level of anteiso lipids at 10°C than was observed, indicative of an additional step beyond FabH influencing fatty acid composition at low temperatures. The potential for control of low temperature growth by feeding compounds that result in the production of butyryl-CoA, the precursor of SCFAs that rigidify the membrane and are incompatible with growth at low temperatures, is recognized.
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Affiliation(s)
- Lauren P Saunders
- School of Biological Sciences, Illinois State University Normal, IL, USA
| | - Suranjana Sen
- School of Biological Sciences, Illinois State University Normal, IL, USA
| | - Brian J Wilkinson
- School of Biological Sciences, Illinois State University Normal, IL, USA
| | - Craig Gatto
- School of Biological Sciences, Illinois State University Normal, IL, USA
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