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Hsu FF. Multiple stage linear ion-trap mass spectrometry toward characterization of native bacterial lipids-a critical review. Biochimie 2023; 215:88-99. [PMID: 37567358 DOI: 10.1016/j.biochi.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/25/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Great strides in the field of lipidomics driven by advances in mass spectrometry techniques in the last decade have moved lipid analysis to a new level and significantly improved our understanding of lipid biochemistry. Multiple stage mass spectrometry (MSn) with high resolution mass spectrometry (HRMS) that allows sequential isolation, fragmentation, and recognition of ion structures, is a powerful tool for characterization of complex and diversified lipid in bacterial cells, in which lipids are often critical for cell aggregation and dissociation, and play important biological roles. In addition to common phospholipids, many bacteria contain unique lipids that are specific to the bacterium genus and even to the bacterium species. In this review, application of linear ion-trap (LIT) MSn in the structural characterization of native bacterial lipids including (1) novel lipids consisting of many isomeric structures, (2) lipids with unique functional groups and modification, (3) complex sphingolipids, peptidolipids, and lipocyclopeptides from various bacteria are presented. LIT MSn approach affords realization of the mechanisms underlying the fragmentation processes, resulting in identification of complex lipid structures that would be very difficult to define using other analytical methods.
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Affiliation(s)
- Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Box 8127, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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2
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Livieri AL, Colaccini F, Hernández MA, Gago G, Alvarez HM, Gramajo H, Rodriguez E. Genetic analysis of acyl-CoA carboxylases involved in lipid accumulation in Rhodococcus jostii RHA1. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12674-2. [PMID: 37439834 DOI: 10.1007/s00253-023-12674-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
In actinomycetes, the acyl-CoA carboxylases, including the so-called acetyl-CoA carboxylases (ACCs), are biotin-dependent enzymes that exhibit broad substrate specificity and diverse domain and subunit arrangements. Bioinformatic analyses of the Rhodococcus jostii RHA1 genome found that this microorganism contains a vast arrange of putative acyl-CoA carboxylases domains and subunits. From the thirteen putative carboxyltransferase domains, only the carboxyltransferase subunit RO01202 and the carboxyltransferase domain present in the multidomain protein RO04222 are highly similar to well-known essential ACC subunits from other actinobacteria. Mutant strains in each of these genes showed that none of these enzymes is essential for R. jostii growth in rich or in minimal media with high nitrogen concentration, presumably because of their partial overlapping activities. A mutant strain in the ro04222 gene showed a decrease in triacylglycerol and mycolic acids accumulation in rich and minimal medium, highlighting the relevance of this multidomain ACC in the biosynthesis of these lipids. On the other hand, RO01202, a carboxyltransferase domain of a putative ACC complex, whose biotin carboxylase and biotin carboxyl carrier protein domain were not yet identified, was found to be essential for R. jostii growth only in minimal medium with low nitrogen concentration. The results of this study have identified a new component of the TAG-accumulating machinery in the oleaginous R. jostii RHA1. While non-essential for growth and TAG biosynthesis in RHA1, the activity of RO04222 significantly contributes to lipogenesis during single-cell oil production. Furthermore, this study highlights the high functional diversity of ACCs in actinobacteria, particularly regarding their essentiality under different environmental conditions. KEY POINTS: • R. jostii possess a remarkable heterogeneity in their acyl-carboxylase complexes. • RO04222 is a multidomain acetyl-CoA carboxylase involved in lipid accumulation. • RO01202 is an essential carboxyltransferase only at low nitrogen conditions.
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Affiliation(s)
- Andrea L Livieri
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Facundo Colaccini
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martin A Hernández
- Instituto de Biociencias de La Patagonia, Facultad de Ciencias Naturales y Ciencias de La Salud, Universidad Nacional de La Patagonia San Juan Bosco y CONICET, Comodoro Rivadavia, Argentina
| | - Gabriela Gago
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Héctor M Alvarez
- Instituto de Biociencias de La Patagonia, Facultad de Ciencias Naturales y Ciencias de La Salud, Universidad Nacional de La Patagonia San Juan Bosco y CONICET, Comodoro Rivadavia, Argentina
| | - Hugo Gramajo
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Eduardo Rodriguez
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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3
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Wood PL, Erol E. Construction of a Bacterial Lipidomics Analytical Platform: Pilot Validation with Bovine Paratuberculosis Serum. Metabolites 2023; 13:809. [PMID: 37512516 PMCID: PMC10383236 DOI: 10.3390/metabo13070809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Lipidomics analyses of bacteria offer the potential to detect and monitor infections in a host since many bacterial lipids are not present in mammals. To evaluate this omics approach, we first built a database of bacterial lipids for representative Gram-positive and Gram-negative bacteria. Our lipidomics analysis of the reference bacteria involved high-resolution mass spectrometry and electrospray ionization with less than a 1.0 ppm mass error. The lipidomics profiles of bacterial cultures clearly distinguished between Gram-positive and Gram-negative bacteria. In the case of bovine paratuberculosis (PTB) serum, we monitored two unique bacterial lipids that we also monitored in Mycobacterium avian subspecies PTB. These were PDIM-B C82, a phthiodiolone dimycocerosate, and the trehalose monomycolate hTMM 28:1, constituents of the bacterial cell envelope in mycolic-containing bacteria. The next step will be to determine if lipidomics can detect subclinical PTB infections which can last 2-to-4 years in bovine PTB. Our data further suggest that it will be worthwhile to continue building our bacterial lipidomics database and investigate the further utility of this approach in other infections of veterinary and human clinical interest.
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Affiliation(s)
- Paul L Wood
- Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy, Harrogate, TN 37752, USA
| | - Erdal Erol
- Department of Veterinary Science, Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40546, USA
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Frankfater C, Fujiwara H, Williams SJ, Minnaard A, Hsu FF. Characterization of Mycobacterium tuberculosis Mycolic Acids by Multiple-Stage Linear Ion-Trap Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:149-159. [PMID: 34842433 DOI: 10.1021/jasms.1c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mycobacterium tuberculosis (Mtb) cells are known to synthesize very long chain (C60-90) structurally complex mycolic acids with various functional groups. In this study, we applied linear ion-trap (LIT) multiple-stage mass spectrometry (MSn), combined with high-resolution mass spectrometry to study the mechanisms underlying the fragmentation processes of mycolic acid standards desorbed as lithiated adduct ions by ESI. This is followed by structural characterization of a Mtb mycolic acid family (Bovine strain). Using the insight fragmentation processes gained from the study, we are able to achieve a near complete characterization of the whole mycolic acid family, revealing the identity of the α-alkyl chain, the location of the functional groups including methyl, methoxy, and keto groups along the meroaldehyde chain in each lipid species. This study showcased the power of LIT MSn toward structural determination of complex lipids in a mixture, which would be otherwise very difficult to define using other analytical techniques.
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Affiliation(s)
- Cheryl Frankfater
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 United States
| | - Hideji Fujiwara
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 United States
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Adriaan Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 United States
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Schaffert L, Ruwe M, Milse J, Hanuschka K, Ortseifen V, Droste J, Brandt D, Schlüter L, Kutter Y, Vinke S, Viehöfer P, Jacob L, Lübke NC, Schulte-Berndt E, Hain C, Linder M, Schmidt P, Wollenschläger L, Luttermann T, Thieme E, Hassa J, Haak M, Wittchen M, Mentz A, Persicke M, Busche T, Rückert C. Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34342562 DOI: 10.1099/ijsem.0.004933] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel corynebacterial species were isolated from soil sampled at a paddock in Vilsendorf, North Rhine-Westphalia, Germany. The strains were coccoid or irregular rod-shaped, catalase-positive and pale white to yellow-orange in colour. By whole genome sequencing and comparison of the 16S rRNA genes as well as the whole genome structure, it was shown that all three strains represent novel species of the family Corynebacteriaceae, order Corynebacteriales, class Actinobacteria. This project describes the isolation, identification, sequencing, and phenotypic characterization of the three novel Corynebacterium species. We propose the names Corynebacterium kalinowskii sp. nov. (DSM 110639T=LMG 31801T), Corynebacterium comes sp. nov. (DSM 110640T=LMG 31802T), and Corynebacterium occultum sp. nov. (DSM 110642T=LMG 31803T).
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Affiliation(s)
- Lena Schaffert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Matthias Ruwe
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Johanna Milse
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Katharina Hanuschka
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Vera Ortseifen
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Proteome and Metabolome Research, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Julian Droste
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - David Brandt
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Laura Schlüter
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Yvonne Kutter
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Svenja Vinke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Prisca Viehöfer
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Lucas Jacob
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Nils-Christian Lübke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Eva Schulte-Berndt
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Carsten Hain
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marten Linder
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Pascal Schmidt
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Lars Wollenschläger
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias Luttermann
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Eric Thieme
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Julia Hassa
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Markus Haak
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Manuel Wittchen
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Almut Mentz
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Characterization of the Uncommon Lipid Families in Corynebacterium glutamicum by Mass Spectrometry. Methods Mol Biol 2021. [PMID: 33954950 DOI: 10.1007/978-1-0716-1410-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
This book chapter provides readers the step-by-step instruction for cell growth, lipid isolation, and lipid analysis to obtain the lipidome of Corynebacterium glutamicum (C. glutamicum) in the genus Corynebacterium, a biotechnologically important bacterium. We separate the lipid families by preparative HPLC with an analytical C-8 column, followed by linear ion-trap multiple stage mass spectrometry (LIT MSn) with high-resolution mass measurement to define the structures of cytidine diphosphate diacylglycerol (CDP-DAG), glucuronosyl diacylglycerol (GlcA-DAG), α-D-mannopyranosyl-(1 → 4)-α-D-glucuronyl diacylglycerol (Man-GlcA-DAG), 1-mycolyl-2-acyl-phosphatidylglycerol (MA-PG), and acyl trehalose monomycolate (acyl-TMM) whose structures have been previously mis-assigned or not defined by mass spectrometric means. We also define the structures of mycolic acid, phosphatidylglycerol, phosphatidylinositol, cardiolipin, trehalose dimycolate lipids in the cell wall. The similarity of the lipidome to that in the Mycobacterium genera is consistent with the notion that Corynebacterium and Mycobacterium are gram-positive bacteria belonging to the suborder Corynebacterineae.
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Lipid and Lipoarabinomannan Isolation and Characterization. Methods Mol Biol 2021. [PMID: 34235650 DOI: 10.1007/978-1-0716-1460-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The very high content of structurally diverse and biologically active lipids of exotic structures is the hallmark of Mycobacteria. As such the lipid composition is commonly used to characterize mycobacterial strains at the species and type-species levels. The present chapter describes the methods that allow the purification of the most commonly isolated biologically active lipids and those used for analyzing extractable lipids and their constituents, cell wall-linked mycolic acids (MA), and lipoarabinomannan (LAM). These involve various chromatographic techniques and analytical procedures necessary for structural and metabolic studies of mycobacterial lipids. In addition, as the use of physical methods has brought important overhang on chemical structures of the very-long-chain MA, which typify mycobacteria, NMR and mass spectrometry data of these specific fatty acids are included.
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Wang HYJ, Tatituri RVV, Goldner NK, Dantas G, Hsu FF. Unveiling the biodiversity of lipid species in Corynebacteria- characterization of the uncommon lipid families in C. glutamicum and pathogen C. striatum by mass spectrometry. Biochimie 2020; 178:158-169. [PMID: 32659445 DOI: 10.1016/j.biochi.2020.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/21/2020] [Accepted: 07/03/2020] [Indexed: 10/23/2022]
Abstract
Uncommon lipids in biotechnologically important Corynebacterium glutamicum and pathogen Corynebacterium striatum in genus Corynebacterium are isolated and identified by linear ion-trap multiple stage mass spectrometry (LIT MSn) with high resolution mass measurement. We redefined several lipid structures that were previously mis-assigned or not defined, including cytidine diphosphate diacylglycerol (CDP-DAG), glucuronosyl diacylglycerol (GlcA-DAG), (α-d-mannopyranosyl)-(1 → 4)-(α-D-glucuronyl diacyglycerol (Man-GlcA-DAG), 1-mycolyl-2-acyl-phosphatidylglycerol (MA-PG), acyl trehalose monomycolate (acyl-TMM). We also report the structures of mycolic acid, phosphatidylglycerol, phosphatidylinositol, cardiolipin, trehalose dimycolate lipids in which many isomeric structures are present. The LIT MSn approaches afford identification of the functional group, the fatty acid substituents and their regiospecificity in the molecules, revealing the biodiversities of the lipid species in two Corynebacterium strains that have played very different and important roles in human nutrition and health.
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Affiliation(s)
- Hay-Yan J Wang
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Raju V V Tatituri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA, 02115, USA
| | - Nicholas K Goldner
- The Edison Family Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63130, USA
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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9
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Frankfater C, Henson WR, Juenger-Leif A, Foston M, Moon TS, Turk J, Kao JLF, Haas A, Hsu FF. Structural Determination of a New Peptidolipid Family from Rhodococcus opacus and the Pathogen Rhodococcus equi by Multiple Stage Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:611-623. [PMID: 31967470 DOI: 10.1021/jasms.9b00059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The cell walls of the genus Rhodococcus including the pathogenic bacterium Rhodococcus equi (R. equi) and biotechnologically important bacterium Rhodococcus opacus (R. opacus) contain an abundant peptidolipid (or termed lipopeptide) family whose structures have not been reported previously. Here, we describe a linear ion-trap multiple-stage mass spectrometric (LIT MSn) approach with high resolution mass spectrometry (HRMS), in conjunction with NMR spectroscopy, chemical reactions, and GC/MS analysis to define the structures of these compounds. We employed LIT MSn (n = 2-8) on the [M + Na]+ ion species to establish the peptide sequence, the identity of the fatty acyl substituent, and its location within the molecule, while NMR spectroscopy and GC/MS were used to recognize the Leu and Ile moieties. The major new lipopeptide found in R. opacus is defined as C17H35CH(OH)CH2CO-NHLeu-Ser-Leu-Ile-Thr-Ile-PheCOOH, where a β-OH fatty acyl (C18-C22) substituent is attached to the N-terminal of the LSLITIF peptide chain via a NH-CO bond. By contrast, the main peptidolipids found in R. equi belong to the cyclopeptidolipid family, which possesses the same peptide sequence and lipid chain, but the β-OH group of the fatty acyl moiety and the C-terminus of the peptide (i.e., the -COOH) are cyclized by an ester bond formation to a lactone, with a structure similar to iturin-A (Peypoux, F. et al. Biochemistry 1978, 17, 3992-3996). The antibiotic activity test of these new lipids did not reveal an activity against any of seven microorganisms tested.
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Affiliation(s)
| | | | - Alexandra Juenger-Leif
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Strasse 61a, 53121 Bonn, Germany
| | | | | | | | | | - Albert Haas
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Strasse 61a, 53121 Bonn, Germany
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Nahar A, Baker AL, Nichols DS, Bowman JP, Britz ML. Application of Thin-Layer Chromatography-Flame Ionization Detection (TLC-FID) to Total Lipid Quantitation in Mycolic-Acid Synthesizing Rhodococcus and Williamsia Species. Int J Mol Sci 2020; 21:ijms21051670. [PMID: 32121355 PMCID: PMC7084869 DOI: 10.3390/ijms21051670] [Citation(s) in RCA: 5] [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: 01/09/2020] [Revised: 02/15/2020] [Accepted: 02/25/2020] [Indexed: 12/25/2022] Open
Abstract
In addition to cell membrane phospholipids, Actinobacteria in the order Corynebacteriales possess a waxy cell envelope containing mycolic acids (MA). In optimized culture condition, some species can also accumulate high concentrations of intracellular triacylglycerols (TAG), which are a potential source of biodiesel. Bacterial lipid classes and composition alter in response to environmental stresses, including nutrient availability, thus understanding carbon flow into different lipid classes is important when optimizing TAG synthesis. Quantitative and qualitative analysis of lipid classes normally requires combinations of different extraction, derivatization, chromatographic and detection methods. In this study, a single-step thin-layer chromatography-flame ionization detection (TLC-FID) technique was applied to quantify lipid classes in six sub-Antarctic Corynebacteriales strains identified as Rhodococcus and Williamsia species. A hexane:diethyl-ether:acetic acid solvent system separated the total cellular lipids extracted from cells lysed by bead beating, which released more bound and unbound MA than sonication. Typical profiles included a major broad non-polar lipid peak, TAG and phospholipids, although trehalose dimycolates, when present, co-eluted with phospholipids. Ultra-performance liquid chromatography-tandem mass-spectrometry and nuclear magnetic resonance spectroscopy detected MA signatures in the non-polar lipid peak and indicated that these lipids were likely bound, at least in part, to sugars from cell wall arabinogalactan. Waxy esters were not detected. The single-solvent TLC-FID procedure provides a useful platform for the quantitation and preliminary screening of cellular lipid classes when testing the impacts of growth conditions on TAG synthesis.
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Affiliation(s)
- Akhikun Nahar
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
| | - Anthony L. Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
| | - David S. Nichols
- Central Science Laboratory, Division of Research, University of Tasmania, Hobart, TAS 7005, Australia;
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
| | - Margaret L. Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.N.); (A.L.B.); (J.P.B.)
- Correspondence:
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11
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Author’s Response. Transplant Proc 2020; 52:424-425. [DOI: 10.1016/j.transproceed.2019.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Study of the conformational behaviour of trehalose mycolates by FT-IR spectroscopy. Chem Phys Lipids 2019; 223:104789. [DOI: 10.1016/j.chemphyslip.2019.104789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/22/2019] [Accepted: 06/25/2019] [Indexed: 11/24/2022]
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13
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Henson WR, Hsu FF, Dantas G, Moon TS, Foston M. Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:339. [PMID: 30607174 PMCID: PMC6309088 DOI: 10.1186/s13068-018-1337-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Lignin is a recalcitrant aromatic polymer that is a potential feedstock for renewable fuel and chemical production. Rhodococcus opacus PD630 is a promising strain for the biological upgrading of lignin due to its ability to tolerate and utilize lignin-derived aromatic compounds. To enhance its aromatic tolerance, we recently applied adaptive evolution using phenol as a sole carbon source and characterized a phenol-adapted R. opacus strain (evol40) and the wild-type (WT) strain by whole genome and RNA sequencing. While this effort increased our understanding of the aromatic tolerance, the tolerance mechanisms were not completely elucidated. RESULTS We hypothesize that the composition of lipids plays an important role in phenol tolerance. To test this hypothesis, we applied high-resolution mass spectrometry analysis to lipid samples obtained from the WT and evol40 strains grown in 1 g/L glucose (glucose), 0.75 g/L phenol (low phenol), or 1.5 g/L phenol (high phenol, evol40 only) as a sole carbon source. This analysis identified > 100 lipid species of mycolic acids, phosphatidylethanolamines (PEs), phosphatidylinositols (PIs), and triacylglycerols. In both strains, mycolic acids had fewer double bond numbers in phenol conditions than the glucose condition, and evol40 had significantly shorter mycolic acid chain lengths than the WT strain in phenol conditions. These results indicate that phenol adaptation affected mycolic acid membrane composition. In addition, the percentage of unsaturated phospholipids decreased for both strains in phenol conditions compared to the glucose condition. Moreover, the PI content increased for both strains in the low phenol condition compared to the glucose condition, and the PI content increased further for evol40 in the high phenol condition relative to the low phenol condition. CONCLUSIONS This work represents the first comprehensive lipidomic study on the membrane of R. opacus grown using phenol as a sole carbon source. Our results suggest that the alteration of the mycolic acid and phospholipid membrane composition may be a strategy of R. opacus for phenol tolerance.
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Affiliation(s)
- William R. Henson
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108 USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - Marcus Foston
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 USA
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14
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Abstract
Corynebacterium diphtheriae, Corynebacterium pseudotuberculosis and Corynebacterium ulcerans share one distinctive feature: they are all putative carriers of the diphtheria toxin (DT), encoded by a β-corynephage integrated into the genome. Due to its medical relevance, C. diphtheriae may be the most highly investigated species of the genus Corynebacterium. Nevertheless, systemic infections caused by C. ulcerans are increasingly being reported indicating that this species is an emerging pathogen today. C. diphtheriae, C. pseudotuberculosis and C. ulcerans are able to colonize different types of epithelial cells in a strain-specific manner, independent of the presence of the tox gene. However, the molecular mechanisms contributing to host colonization are barely understood. This review gives a comprehensive update of recent data concerning the adhesion properties of toxigenic corynebacteria, demonstrating that adhesion is a multi-factorial process.
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Affiliation(s)
- Lisa Ott
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Professur für Mikrobiologie, Staudtstr. 5, 91058 Erlangen, Germany
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15
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Xiong LB, Liu HH, Xu LQ, Sun WJ, Wang FQ, Wei DZ. Improving the production of 22-hydroxy-23,24-bisnorchol-4-ene-3-one from sterols in Mycobacterium neoaurum by increasing cell permeability and modifying multiple genes. Microb Cell Fact 2017; 16:89. [PMID: 28532497 PMCID: PMC5440992 DOI: 10.1186/s12934-017-0705-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/15/2017] [Indexed: 12/04/2022] Open
Abstract
Background The strategy of modifying the sterol catabolism pathway in mycobacteria has been adopted to produce steroidal pharmaceutical intermediates, such as 22-hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC), which is used to synthesize various steroids in the industry. However, the productivity is not desirable due to some inherent problems, including the unsatisfactory uptake rate and the low metabolic efficiency of sterols. The compact cell envelope of mycobacteria is a main barrier for the uptake of sterols. In this study, a combined strategy of improving the cell envelope permeability as well as the intracellular sterol metabolism efficiency was investigated to increase the productivity of 4-HBC. Results MmpL3, encoding a transmembrane transporter of trehalose monomycolate, is an important gene influencing the assembly of mycobacterial cell envelope. The disruption of mmpL3 in Mycobacterium neoaurum ATCC 25795 significantly enhanced the cell permeability by 23.4% and the consumption capacity of sterols by 15.6%. Therefore, the inactivation of mmpL3 was performed in a 4-HBC-producing strain derived from the wild type M. neoaurum and the 4-HBC production in the engineered strain was increased by 24.7%. Subsequently, to enhance the metabolic efficiency of sterols, four key genes, choM1, choM2, cyp125, and fadA5, involved in the sterol conversion pathway were individually overexpressed in the engineered mmpL3-deficient strain. The production of 4-HBC displayed the increases of 18.5, 8.9, 14.5, and 12.1%, respectively. Then, the more efficient genes (choM1, cyp125, and fadA5) were co-overexpressed in the engineered mmpL3-deficient strain, and the productivity of 4-HBC was ultimately increased by 20.3% (0.0633 g/L/h, 7.59 g/L 4-HBC from 20 g/L phytosterol) compared with its original productivity (0.0526 g/L/h, 6.31 g/L 4-HBC from 20 g/L phytosterol) in an industrial resting cell bio-transformation system. Conclusions Increasing cell permeability combined with the co-overexpression of the key genes (cyp125, choM1, and fadA5) involved in the conversion pathway of sterol to 4-HBC was effective to enhance the productivity of 4-HBC. The strategy might also be useful for the conversion of sterol to other steroidal intermediates by mycobacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0705-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liang-Bin Xiong
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Hao-Hao Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Li-Qin Xu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Wan-Ju Sun
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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16
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Lin MH, Miner JH, Turk J, Hsu FF. Linear ion-trap MS n with high-resolution MS reveals structural diversity of 1-O-acylceramide family in mouse epidermis. J Lipid Res 2017; 58:772-782. [PMID: 28154204 DOI: 10.1194/jlr.d071647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 01/27/2017] [Indexed: 12/30/2022] Open
Abstract
1-O-acylceramide is a new class of epidermal cer-amide (Cer) found in humans and mice. Here, we report an ESI linear ion-trap (LIT) multiple-stage MS (MSn) approach with high resolution toward structural characterization of this lipid family isolated from mice. Molecular species desorbed as the [M + H]+ ions were subjected to LIT MS2 to yield predominately the [M + H - H2O]+ ions, followed by MS3 to cleave the 1-O-acyl residue to yield the [M + H - H2O - (1-O-FA)]+ ions. The structures of the N-acyl chain and long-chain base (LCB) of the molecule were determined by MS4 on [M + H - H2O - (1-O-FA)]+ ions that yielded multiple sets of specific ions. Using this approach, isomers varied in the 1-O-acyl (from 14:0- to 30:0-O-acyl) and N-acyl chains (from 14:0- to 34:1-N-acyl) with 18:1-sphingosine as the major LCB were found for the entire family. Minor isomers consisting of 16:1-, 17:1-, 18:2-, and 19:1-sphingosine LCBs with odd fatty acyl chain or with monounsaturated N- or O-fatty acyl substituents were also identified. An estimation of more than 700 1-O-acylceramide species, largely isobaric isomers, are present, underscoring the complexity of this Cer family.
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Affiliation(s)
- Meei-Hua Lin
- Division of Nephrology Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Jeffrey H Miner
- Division of Nephrology Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - John Turk
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO.
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17
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Marshall DL, Saville JT, Maccarone AT, Ailuri R, Kelso MJ, Mitchell TW, Blanksby SJ. Determination of ester position in isomeric (O-acyl)-hydroxy fatty acids by ion trap mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2351-2359. [PMID: 27520617 DOI: 10.1002/rcm.7715] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/08/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE (O-acyl)-hydroxy fatty acids (OAHFAs) are a recently discovered class of endogenous lipids, generating significant interest for their correlation with enhanced glucose tolerance. Structural variants that differ in the position of the ester linkage have been described, including the ω-OAHFA sub-class, that plays a key role in stabilizing the human tear film. Developing analytical tools for rapid and unambiguous structural elucidation of OAHFAs is essential to understanding their diverse physiological functions. METHODS Commercially available and synthesized OAHFA standards were dissolved in chloroform and subsequently diluted into methanol with 1.5 mM ammonium acetate. Negative ion collision-induced dissociation (CID) MSn spectra were acquired using chip-based nano-electrospray ionization (Advion TriVersa NanoMate) coupled to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific). RESULTS Major product ions observed during CID of [OAHFA - H]- ions readily identify the constituent fatty acid and hydroxy fatty acid; however, isomers are not easily distinguished. Interrogation of the hydroxy fatty acid and dehydrated hydroxy fatty acid product ions by MSn and ion-molecule reactions yielded diagnostic ions that readily pinpoint hydroxylation position and, thus, the OAHFA ester location. Conversely, these ions are characteristically absent in the MS3 spectra of ω-OAHFAs. Unimolecular dissociation mechanisms are proposed, which are shown to be consistent with prior isotopic labelling experiments. CONCLUSIONS A mechanistic rationale is provided to explain the unimolecular dissociation of [OAHFA - H]- ions in an ion trap mass spectrometer, thus enabling near-complete de novo structural elucidation of OAHFAs in shotgun lipidomics workflows, even if synthetic standards are unavailable for comparison. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- David L Marshall
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
| | - Jennifer T Saville
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Alan T Maccarone
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Ramesh Ailuri
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Michael J Kelso
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Todd W Mitchell
- School of Medicine, University of Wollongong, Wollongong, NSW, 2522, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Stephen J Blanksby
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
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18
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Crick PJ, Guan XL. Lipid metabolism in mycobacteria--Insights using mass spectrometry-based lipidomics. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1861:60-67. [PMID: 26515252 DOI: 10.1016/j.bbalip.2015.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/14/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022]
Abstract
Diseases including tuberculosis and leprosy are caused by species of the Mycobacterium genus and are a huge burden on global health, aggravated by the emergence of drug resistant strains. Mycobacteria have a high lipid content and complex lipid profile including several unique classes of lipid. Recent years have seen a growth in research focused on lipid structures, metabolism and biological functions driven by advances in mass spectrometry techniques and instrumentation, particularly the use of electrospray ionization. Here we review the contributions of lipidomics towards the advancement of our knowledge of lipid metabolism in mycobacterial species.
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Affiliation(s)
- Peter J Crick
- Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland; University of Basel, CH-4000 Basel, Switzerland
| | - Xue Li Guan
- Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland; University of Basel, CH-4000 Basel, Switzerland; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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19
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Abstract
Mycobacteria are microorganisms that contain a very high content of structurally diverse lipids, some of them being biologically active substances. As such the lipid composition is commonly used to characterize mycobacterial strains at the species and type-species level. This chapter describes the methods that allow the purification of the most commonly isolated biologically active lipids and those used for analyzing extractable lipids and their constituents, cell wall-linked mycolic acids and lipoarabinomannan (LAM). The latter involve simple chromatographic and analytical techniques, such as thin-layer chromatography and gas chromatography coupled to mass spectrometry.
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Affiliation(s)
- Marie-Antoinette Lanéelle
- Tuberculosis & Infection Biology Department, Institut de Pharmacologie et de BiologieStructurale (IPBS), Centre National de la Recherche Scientifique (CNRS), BP 64182, 205 route de Narbonne, 31077, Toulouse, France
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20
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Mycolic acids: structures, biosynthesis, and beyond. ACTA ACUST UNITED AC 2013; 21:67-85. [PMID: 24374164 DOI: 10.1016/j.chembiol.2013.11.011] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/04/2013] [Accepted: 11/27/2013] [Indexed: 11/24/2022]
Abstract
Mycolic acids are major and specific lipid components of the mycobacterial cell envelope and are essential for the survival of members of the genus Mycobacterium that contains the causative agents of both tuberculosis and leprosy. In the alarming context of the emergence of multidrug-resistant, extremely drug-resistant, and totally drug-resistant tuberculosis, understanding the biosynthesis of these critical determinants of the mycobacterial physiology is an important goal to achieve, because it may open an avenue for the development of novel antimycobacterial agents. This review focuses on the chemistry, structures, and known inhibitors of mycolic acids and describes progress in deciphering the mycolic acid biosynthetic pathway. The functional and key biological roles of these molecules are also discussed, providing a historical perspective in this dynamic area.
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21
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Balogun MO, Huws EH, Sirhan MM, Saleh AD, Dulayymi JRA, Pilcher L, Verschoor JA, Baird MS. Thiol modified mycolic acids. Chem Phys Lipids 2013; 172-173:40-55. [DOI: 10.1016/j.chemphyslip.2013.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/21/2013] [Accepted: 03/23/2013] [Indexed: 11/30/2022]
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22
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Sabareesh V, Singh G. Mass spectrometry based lipid(ome) analyzer and molecular platform: a new software to interpret and analyze electrospray and/or matrix-assisted laser desorption/ionization mass spectrometric data of lipids: a case study from Mycobacterium tuberculosis. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:465-477. [PMID: 23584940 DOI: 10.1002/jms.3163] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 12/23/2012] [Accepted: 12/30/2012] [Indexed: 06/02/2023]
Abstract
Mass Spectrometry based Lipid(ome) Analyzer and Molecular Platform (MS-LAMP) is a new software capable of aiding in interpreting electrospray ionization (ESI) and/or matrix-assisted laser desorption/ionization (MALDI) mass spectrometric data of lipids. The graphical user interface (GUI) of this standalone programme is built using Perl::Tk. Two databases have been developed and constituted within MS-LAMP, on the basis of Mycobacterium tuberculosis (M. tb) lipid database (www.mrl.colostate.edu) and that of Lipid Metabolites and Pathways Strategy Consortium (LIPID MAPS; www.lipidmaps.org). Different types of queries entered through GUI would interrogate with a chosen database. The queries can be molecular mass(es) or mass-to-charge (m/z) value(s) and molecular formula. LIPID MAPS identifier also can be used to search but not for M. tb lipids. Multiple choices have been provided to select diverse ion types and lipids. Satisfying to input parameters, a glimpse of various lipid categories and their population distribution can be viewed in the output. Additionally, molecular structures of lipids in the output can be seen using ChemSketch (www.acdlabs.com), which has been linked to the programme. Furthermore, a version of MS-LAMP for use in Linux operating system is separately available, wherein PyMOL can be used to view molecular structures that result as output from General Lipidome MS-LAMP. The utility of this software is demonstrated using ESI mass spectrometric data of lipid extracts of M. tb grown under two different pH (5.5 and 7.0) conditions.
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Affiliation(s)
- Varatharajan Sabareesh
- Proteomics and Structural Biology Unit, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, New Delhi, 110007, India.
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23
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Sydor T, von Bargen K, Hsu FF, Huth G, Holst O, Wohlmann J, Becken U, Dykstra T, Söhl K, Lindner B, Prescott JF, Schaible UE, Utermöhlen O, Haas A. Diversion of phagosome trafficking by pathogenic Rhodococcus equi depends on mycolic acid chain length. Cell Microbiol 2012; 15:458-73. [PMID: 23078612 PMCID: PMC3864644 DOI: 10.1111/cmi.12050] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 09/19/2012] [Accepted: 10/11/2012] [Indexed: 12/30/2022]
Abstract
Rhodococcus equi is a close relative of Mycobacterium spp. and a facultative intracellular pathogen which arrests phagosome maturation in macrophages before the late endocytic stage. We have screened a transposon mutant library of R. equi for mutants with decreased capability to prevent phagolysosome formation. This screen yielded a mutant in the gene for β-ketoacyl-(acyl carrier protein)-synthase A (KasA), a key enzyme of the long-chain mycolic acid synthesizing FAS-II system. The longest kasA mutant mycolic acid chains were 10 carbon units shorter than those of wild-type bacteria. Coating of non-pathogenic E. coli with purified wild-type trehalose dimycolate reduced phagolysosome formation substantially which was not the case with shorter kasA mutant-derived trehalose dimycolate. The mutant was moderately attenuated in macrophages and in a mouse infection model, but was fully cytotoxic.Whereas loss of KasA is lethal in mycobacteria, R. equi kasA mutant multiplication in broth was normal proving that long-chain mycolic acid compounds are not necessarily required for cellular integrity and viability of the bacteria that typically produce them. This study demonstrates a central role of mycolic acid chain length in diversion of trafficking by R. equi.
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Affiliation(s)
- Tobias Sydor
- Institute for Cell Biology, University of Bonn, Bonn, Germany
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Hsu FF, Pacheco S, Turk J, Purdy G. Structural determination of glycopeptidolipids of Mycobacterium smegmatis by high-resolution multiple-stage linear ion-trap mass spectrometry with electrospray ionization. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1269-1281. [PMID: 23019158 PMCID: PMC3462375 DOI: 10.1002/jms.3070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Glycopeptidolipids (GPLs) are abundant in the cell walls of different species of mycobacteria and consist of tripeptide-amino-alcohol core of D-Phe-D-allo-Thr-D-Ala-L-alaninol linked to 3-hydroxy or 3-methoxy C(26-34) fatty acyl chain at the N-terminal of D-Phe via amide linkage, and a 6-deoxytalose (6-dTal) and an O-methyl rhamnose residues, respectively, attach to D-allo-Thr and the terminal L-alaninol. They are important cell-surface antigens that are implicated in the pathogenesis of opportunistic mycobacteria belonging to the Mycobacterium avium complex. In this contribution, we described multiple-stage linear ion trap in conjunction with high-resolution mass spectrometry towards structural characterization of complex GPLs as [M + Na](+) ions isolated from Mycobacterium smegmatis, a fast-growing and non-pathogenic mycobacterial species. Following resonance excitation in an ion trap, MS(n) spectra of the [M + Na](+) ions of GPLs contained mainly b and y series ions that readily determine the peptide sequence. Fragment ions from MS(n) also afford locating the 6-dTal and O-methyl rhamnose residues linked to the D-allo-Thr and terminal L-alaninol of the peptide core, respectively, as well as recognizing the modifications of the glycosides, including their acetylation and methylation states and the presence of succinyl group. The GPL families consisting of 3-hydroxy fatty acyl and of 3-methoxy fatty acyl substituents are readily distinguishable. The MS profiles of the GPLs from cells are dependant on the conditions they were grown, and several isobaric isomers were identified for many of the molecular species. These multiple-stage mass spectrometric approaches give detailed structures of GPL in complex mixtures of which the isomeric structures are difficult to define using other analytical methods.
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Affiliation(s)
- Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Hartler J, Tharakan R, Köfeler HC, Graham DR, Thallinger GG. Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data. Brief Bioinform 2012; 14:375-90. [PMID: 22764120 DOI: 10.1093/bib/bbs030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently occurring isobaric and isomeric lipid species complicate lipidomics analyses from an analytical and bioinformatics perspective. Various MS/MS strategies have evolved to resolve ambiguous identifications of lipid species, and these strategies have been supported by corresponding bioinformatics analysis tools. This review intends to familiarize readers with available bioinformatics MS/MS analysis tools and databases, the structural information obtainable from these, and their applicability to different MS/MS strategies. Finally, future challenges in detecting double bond positions are investigated from a bioinformatics perspective.
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26
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Hong S, Cheng TY, Layre E, Sweet L, Young DC, Posey JE, Butler WR, Moody DB. Ultralong C100 mycolic acids support the assignment of Segniliparus as a new bacterial genus. PLoS One 2012; 7:e39017. [PMID: 22720018 PMCID: PMC3375245 DOI: 10.1371/journal.pone.0039017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 05/15/2012] [Indexed: 11/19/2022] Open
Abstract
Mycolic acid-producing bacteria isolated from the respiratory tract of human and non-human mammals were recently assigned as a distinct genus, Segniliparus, because they diverge from rhodococci and mycobacteria in genetic and chemical features. Using high accuracy mass spectrometry, we determined the chemical composition of 65 homologous mycolic acids in two Segniliparus species and separately analyzed the three subclasses to measure relative chain length, number and stereochemistry of unsaturations and cyclopropyl groups within each class. Whereas mycobacterial mycolate subclasses are distinguished from one another by R groups on the meromycolate chain, Segniliparus species synthesize solely non-oxygenated α-mycolates with high levels of cis unsaturation. Unexpectedly Segniliparus α-mycolates diverge into three subclasses based on large differences in carbon chain length with one bacterial culture producing mycolates that range from C58 to C100. Both the overall chain length (C100) and the chain length diversity (C42) are larger than previously seen for mycolic acid-producing organisms and provide direct chemical evidence for assignment of Segniliparus as a distinct genus. Yet, electron microscopy shows that the long and diverse mycolates pack into a typical appearing membrane. Therefore, these new and unexpected extremes of mycolic acid chemical structure raise questions about the modes of mycolic acid packing and folding into a membrane.
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Affiliation(s)
- Sunhee Hong
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Emilie Layre
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lindsay Sweet
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - David C. Young
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - W. Ray Butler
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (DBM); (WRB)
| | - D. Branch Moody
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (DBM); (WRB)
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Verschoor JA, Baird MS, Grooten J. Towards understanding the functional diversity of cell wall mycolic acids of Mycobacterium tuberculosis. Prog Lipid Res 2012; 51:325-39. [PMID: 22659327 DOI: 10.1016/j.plipres.2012.05.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 03/05/2012] [Accepted: 05/23/2012] [Indexed: 01/08/2023]
Abstract
Mycolic acids constitute the waxy layer of the outer cell wall of Mycobacterium spp. and a few other genera. They are diverse in structure, providing a unique chromatographic foot-print for almost each of the more than 70 Mycobacterium species. Although mainly esterified to cell wall arabinogalactan, trehalose or glucose, some free mycolic acid is secreted during in vitro growth of Mycobacterium tuberculosis. In M. tuberculosis, α-, keto- and methoxy-mycolic acids are the main classes, each differing in their ability to attract neutrophils, induce foamy macrophages or adopt an antigenic structure for antibody recognition. Of interest is their particular relationship to cholesterol, discovered by their ability to attract cholesterol, to bind Amphotericin B or to be recognised by monoclonal antibodies that cross-react with cholesterol. The structural elements that determine this diverse functionality include the carboxylic acid in the mycolic motif, as well as the nature and stereochemistry of the two functional groups in the merochain. The functional diversity of mycolic acid classes implies that much information may be contained in the selective expression and secretion of mycolic acids to establish tuberculosis after infection of the host. Their cholesteroid nature may relate to how they utilize host cholesterol for their persistent survival.
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Affiliation(s)
- Jan A Verschoor
- Department Biochemistry, University of Pretoria, Pretoria 0002, South Africa.
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Kolouchová I, Schreiberová O, Masák J, Sigler K, Řezanka T. Structural analysis of mycolic acids from phenol-degrading strain of Rhodococcus erythropolis by liquid chromatography–tandem mass spectrometry. Folia Microbiol (Praha) 2012; 57:473-83. [DOI: 10.1007/s12223-012-0156-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 04/24/2012] [Indexed: 11/30/2022]
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Lanéelle MA, Launay A, Spina L, Marrakchi H, Laval F, Eynard N, Lemassu A, Tropis M, Daffé M, Etienne G. A novel mycolic acid species defines two novel genera of the Actinobacteria, Hoyosella and Amycolicicoccus. Microbiology (Reading) 2012; 158:843-855. [DOI: 10.1099/mic.0.055509-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Marie-Antoinette Lanéelle
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Anne Launay
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Lucie Spina
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Hedia Marrakchi
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Françoise Laval
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Nathalie Eynard
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Anne Lemassu
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Maryelle Tropis
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Mamadou Daffé
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
| | - Gilles Etienne
- Université de Toulouse (Université Paul Sabatier Toulouse III), IPBS, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
- Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et de Biologie Structurale (IPBS, Unité Mixte de Recherche 5089) Département Mécanismes Moléculaires des Infections Mycobactériennes, 205 Route de Narbonne, BP 64182, F-31077 Toulouse, France
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30
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Hsu FF, Wohlmann J, Turk J, Haas A. Structural definition of trehalose 6-monomycolates and trehalose 6,6'-dimycolates from the pathogen Rhodococcus equi by multiple-stage linear ion-trap mass spectrometry with electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2160-2170. [PMID: 21972013 PMCID: PMC3938585 DOI: 10.1007/s13361-011-0240-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 08/18/2011] [Accepted: 08/22/2011] [Indexed: 05/31/2023]
Abstract
The cell wall of the pathogenic bacterium Rhodococcus equi (R. equi) contains abundant trehalose monomycolate (TMM) and trehalose dimycolate (TDM), the glycolipids bearing mycolic acids. Here, we describe multiple-stage (MS(n)) linear ion-trap (LIT) mass spectrometric approaches toward structural characterization of TMM and TDM desorbed as [M + Alk](+) (Alk = Na, Li) and as [M + X](-) (X = CH(3)CO(2), HCO(2)) ions by electrospray ionization (ESI). Upon MS(n) (n=2, 3, 4) on the [M + Alk](+) or the [M + X](-) adduct ions of TMM and TDM, abundant structurally informative fragment ions are readily available, permitting fast assignment of the length of the meromycolate chain and of the α-branch on the mycolyl residues. In this way, structures of TMM and TDM isolated from pathogenic R. equi strain 103 can be determined. Our results indicate that the major TMM and TDM molecules possess 6, and/or 6'-mycolyl groups that consist of mainly C14 and C16 α-branches with meromycolate branches ranging from C18 to C28, similar to the structures of the unbound mycolic acids found in the cell envelope. Up to 60 isobaric isomers varying in chain length of the α-branch and of the meromycolate backbone were observed for some of the TDM species in the mixture. This mass spectrometric approach provides a direct method that affords identification of various TMM and TDM isomers in a mixture of which the complexity of this lipid class has not been previously reported using other analytical methods.
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Affiliation(s)
- Fong-Fu Hsu
- Department of Internal Medicine, Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington University School of Medicine, 660 S Euclid, Box 8127, St. Louis, MO 63110, USA.
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Rhoades ER, Streeter C, Turk J, Hsu FF. Characterization of sulfolipids of Mycobacterium tuberculosis H37Rv by multiple-stage linear ion-trap high-resolution mass spectrometry with electrospray ionization reveals that the family of sulfolipid II predominates. Biochemistry 2011; 50:9135-47. [PMID: 21919534 DOI: 10.1021/bi2012178] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is unique among bacterial pathogens in that it contains a wide array of complex lipids and lipoglycans on its cell wall. Among them, the sulfated glycolipid, termed the sulfolipid, is thought to mediate specific host-pathogen interactions during infection. Sulfolipids (SLs), including sulfolipid I (SL-I) and sulfolipid II (SL-II), are 2,3,6,6'-tetraacyltrehalose 2'-sulfates. SL-I was identified as a family of homologous 2-palmitoyl(stearoyl)-3-phthioceranoyl-6,6'-bis(hydroxyphthioceranoy1)trehalose 2'-sulfates and was believed to be the principal sulfolipid of M. tuberculosis strain H37Rv. We cultured and extracted sulfolipids using various conditions, including those originally described, and employed high-resolution multiple-stage linear ion-trap mass spectrometry with electrospray ionization to characterize the structure of the principal SL. We revealed that SL-II, a family of homologous 2-stearoyl(palmitoyl)-3,6,6'-tris(hydroxyphthioceranoy1)trehalose 2'-sulfates, rather than SL-I is the principal sulfolipid class. We identified a great number of isomers resulting from permutation of the various hydroxyphthioceranoyl substituents at positions 6 and 6' of the trehalose backbone for each of the SL-II species in the entire family. We redefined the structure of this important lipid family that was misassigned using the traditional methods 40 years ago.
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Affiliation(s)
- Elizabeth R Rhoades
- Department of Microbiology and Immunology, C5 109 Vet Medical Center, Cornell University, Ithaca, New York 14853, United States
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Holder JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J, Zeng Q, Leach ALB, Ghiviriga I, Dancel C, Abeel T, Gevers D, Kodira CD, Desany B, Affourtit JP, Birren BW, Sinskey AJ. Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genet 2011; 7:e1002219. [PMID: 21931557 PMCID: PMC3169528 DOI: 10.1371/journal.pgen.1002219] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 06/17/2011] [Indexed: 11/18/2022] Open
Abstract
The Actinomycetales bacteria Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 bioconvert a diverse range of organic substrates through lipid biosynthesis into large quantities of energy-rich triacylglycerols (TAGs). To describe the genetic basis of the Rhodococcus oleaginous metabolism, we sequenced and performed comparative analysis of the 9.27 Mb R. opacus PD630 genome. Metabolic-reconstruction assigned 2017 enzymatic reactions to the 8632 R. opacus PD630 genes we identified. Of these, 261 genes were implicated in the R. opacus PD630 TAGs cycle by metabolic reconstruction and gene family analysis. Rhodococcus synthesizes uncommon straight-chain odd-carbon fatty acids in high abundance and stores them as TAGs. We have identified these to be pentadecanoic, heptadecanoic, and cis-heptadecenoic acids. To identify bioconversion pathways, we screened R. opacus PD630, R. jostii RHA1, Ralstonia eutropha H16, and C. glutamicum 13032 for growth on 190 compounds. The results of the catabolic screen, phylogenetic analysis of the TAGs cycle enzymes, and metabolic product characterizations were integrated into a working model of prokaryotic oleaginy.
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Affiliation(s)
- Jason W. Holder
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Jil C. Ulrich
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anthony C. DeBono
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul A. Godfrey
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Jeremy Zucker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Alex L. B. Leach
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ion Ghiviriga
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Christine Dancel
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Thomas Abeel
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Dirk Gevers
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Brian Desany
- 454 Life Sciences, Branford, Connecticut, United States of America
| | | | - Bruce W. Birren
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Anthony J. Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Engineering Systems Division, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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