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Zhang ZJ, Wu C, Moreira R, Dorantes D, Pappas T, Sundararajan A, Lin H, Pamer EG, van der Donk WA. Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals. ACS Chem Biol 2024; 19:357-369. [PMID: 38293740 PMCID: PMC10877564 DOI: 10.1021/acschembio.3c00577] [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: 09/17/2023] [Revised: 12/12/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024]
Abstract
Recent advances in sequencing techniques unveiled the vast potential of ribosomally synthesized and post-translationally modified peptides (RiPPs) encoded in microbiomes. Class I lantibiotics such as nisin A, widely used as a food preservative, have been investigated for their efficacy in killing pathogens. However, the impact of nisin and nisin-like class I lantibiotics on commensal bacteria residing in the human gut remains unclear. Here, we report six gut-derived class I lantibiotics that are close homologues of nisin, four of which are novel. We applied an improved lantibiotic expression platform to produce and purify these lantibiotics for antimicrobial assays. We determined their minimal inhibitory concentration (MIC) against both Gram-positive human pathogens and gut commensals and profiled the lantibiotic resistance genes in these pathogens and commensals. Structure-activity relationship (SAR) studies with analogs revealed key regions and residues that impact their antimicrobial properties. Our characterization and SAR studies of nisin-like lantibiotics against both pathogens and human gut commensals could shed light on the future development of lantibiotic-based therapeutics and food preservatives.
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Affiliation(s)
- Zhenrun J. Zhang
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
- Department
of Microbiology, University of Chicago, Chicago, Illinois 60637, United States
| | - Chunyu Wu
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Ryan Moreira
- Department
of Chemistry, The Howard Hughes Medical
Institute, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Darian Dorantes
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Téa Pappas
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Anitha Sundararajan
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Huaiying Lin
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Eric G. Pamer
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
- Departments
of Medicine and Pathology, University of
Chicago, Chicago, Illinois 60637, United States
| | - Wilfred A. van der Donk
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, The Howard Hughes Medical
Institute, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
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Townsend JP, Sweeney AM. Catecholic Compounds in Ctenophore Colloblast and Nerve Net Proteins Suggest a Structural Role for DOPA-Like Molecules in an Early-Diverging Animal Lineage. THE BIOLOGICAL BULLETIN 2019; 236:55-65. [PMID: 30707604 DOI: 10.1086/700695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ctenophores, or comb jellies, are among the earliest-diverging extant animal lineages. Several recent phylogenomic studies suggest that they may even be the sister group to all other animals. This unexpected finding remains difficult to contextualize, particularly given ctenophores' unique and sometimes poorly understood physiology. Colloblasts, a ctenophore-specific cell type found on the surface of these animals' tentacles, are emblematic of this difficulty. The exterior of the colloblast is dotted with granules that burst and release an adhesive on contact with prey, ensnaring it for consumption. To date, little is known about the fast-acting underwater adhesive that these cells secrete or its biochemistry. We present evidence that proteins in the colloblasts of the ctenophore Pleurobrachia bachei incorporate catecholic compounds similar to the amino acid l-3,4-dihydroxyphenylalanine. These compounds are associated with adhesive-containing granules on the surface of colloblasts, suggesting that they may play a role in prey capture, akin to dihydroxyphenylalanine-based adhesives in mussel byssus. We also present unexpected evidence of similar catecholic compounds in association with the subepithelial nerve net. There, catecholic compounds are present in spatial patterns similar to those of l-3,4-dihydroxyphenylalanine and its derivatives in cnidarian nerves, where they are associated with membranes and possess unknown functionality. This "structural" use of catecholic molecules in ctenophores represents the earliest-diverging animal lineage in which this trait has been observed, though it remains unclear whether structural catechols are deeply rooted in animals or whether they have arisen multiple times.
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Key Words
- -DOPA, -3,4-dihydroxyphenylalanine
- -diphenols, -diphenols
- AcOH, acetic acid
- CTAB, cetrimonium bromide
- DOPA, dihydroxyphenylalanine
- FIF, formaldehyde-induced fluorescence
- PBS, phosphate-buffered saline
- PFA, paraformaldehyde
- TCA, tricholoracetic acid.
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3
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Duchateau A, van Scheppingen W. Stability study of a nisin/natamycin blend by LC-MS. Food Chem 2018; 266:240-244. [DOI: 10.1016/j.foodchem.2018.05.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/17/2018] [Accepted: 05/27/2018] [Indexed: 01/26/2023]
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Kakkar N, Perez JG, Liu WR, Jewett MC, van der Donk WA. Incorporation of Nonproteinogenic Amino Acids in Class I and II Lantibiotics. ACS Chem Biol 2018; 13:951-957. [PMID: 29439566 PMCID: PMC5910287 DOI: 10.1021/acschembio.7b01024] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lantibiotics are ribosomally synthesized and post-translationally modified peptide natural products that contain thioether cross-links formed by lanthionine and methyllanthionine residues. They exert potent antimicrobial activity against Gram-positive bacteria. We herein report production of analogues of two lantibiotics, lacticin 481 and nisin, that contain nonproteinogenic amino acids using two different strategies involving amber stop codon suppression technology. These methods complement recent alternative approaches to incorporate nonproteinogenic amino acids into lantibiotics.
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Affiliation(s)
- Nidhi Kakkar
- Howard Hughes Medical Institute and Roger Adams Laboratory, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jessica G. Perez
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843m United States
| | - Michael C. Jewett
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Roger Adams Laboratory, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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5
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Improved Pretreatment Method for Determination of Nisins A and Z and Monitoring in Cheese Using Liquid Chromatrography-Tandem Mass Spectrometry. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0158-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Peng J, Zhang L, Gu ZH, Ding ZY, Shi GY. The role of nisin in fuel ethanol production with Saccharomyces cerevisiae. Lett Appl Microbiol 2012; 55:128-34. [PMID: 22691226 DOI: 10.1111/j.1472-765x.2012.03275.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the effects of nisin on lactobacilli contamination of yeast during ethanol fermentation and to determine the appropriate concentration required to control the growth of selected lactobacilli in a YP/glucose media fermentation model. METHODS AND RESULTS The lowest concentration of nisin tested (5 IU ml(-1) ) effectively controlled the contamination of YP/glucose media with 10(6) CFU ml(-1) lactobacilli. Lactic acid yield decreased from 5.0 to 2. 0 g l(-1) and potential ethanol yield losses owing to the growth and metabolism of Lactobacillus plantarum and Lactobacillus brevis were reduced by 11 and 7.8%, respectively. Approximately, equal concentrations of lactic acid were produced by Lact. plantarum and Lact. brevis in the presence of 5 and 2 IU ml(-1) nisin, respectively, thus demonstrating the relatively higher nisin sensitivity of Lact. brevis for the strains in this study. No differences were observed in the final ethanol concentrations produced by yeast in the absence of bacteria at any of the nisin concentrations tested. CONCLUSIONS Metabolism of contaminating bacteria was reduced in the presence of 5 IU ml(-1) nisin, resulting in reduced lactic acid production and increased ethanol production by the yeast. SIGNIFICANCE AND IMPACT OF THE STUDY Bacteriocins represent an alternative to the use of antibiotics for the control of bacterial contamination in fuel ethanol plants and may be important in preventing the emergence of antibiotic-resistant contaminating strains.
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Affiliation(s)
- J Peng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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7
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Abstract
The lantibiotic nisin has been used as an effective food preservative to combat food-borne pathogens for over 40 y. Despite this successful use, nisin's stability at pH 7 is limited. Herein, we describe a nisin analog encoded on the genome of the thermophilic bacterium Geobacillus thermodenitrificans NG80-2. This analog termed geobacillin I was obtained by heterologous expression in Escherichia coli and subsequent purification. Extensive NMR characterization demonstrated that geobacillin I contains seven thioether cross-links, two more than the five cross-links found in nisin and the most cross-links found in any lantibiotic to date. The antimicrobial spectrum of geobacillin I was generally similar to that of nisin A, with increased activity against Streptococcus dysgalactiae, one of the causative agents of bovine mastitis. Geobacillin I demonstrated increased stability compared to nisin A. In addition to geobacillin I, the genome of G. thermodenitrificans NG80-2 also contains a class II lantibiotic biosynthetic gene cluster. The corresponding compound was produced in E. coli, and has a ring topology different than that of any known lantibiotic as determined by tandem mass spectrometry. Interestingly, geobacillin II only demonstrated antimicrobial activity against Bacillus strains. Seven Geobacillus strains were screened for production of the geobacillins using whole-cell MALDI-MS and five were shown to produce geobacillin I, but none produced geobacillin II.
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8
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Schneider N, Werkmeister K, Pischetsrieder M. Analysis of nisin A, nisin Z and their degradation products by LCMS/MS. Food Chem 2011; 127:847-54. [DOI: 10.1016/j.foodchem.2011.01.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 12/10/2010] [Accepted: 01/01/2011] [Indexed: 10/18/2022]
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9
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Kuiper JL, Shapley PA. Aerobic alcohol oxidation catalyzed by a new, oxygen-bridged heterometallic compound [PPh4][Ru(N)Me2(μ2-O)2Pd((−)-sparteine)]. J Organomet Chem 2007. [DOI: 10.1016/j.jorganchem.2006.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Chapter 10 Technologies interfacing capillary electrophoresis to mass spectrometry. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0166-526x(05)46010-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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11
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Abstract
The application of mass spectrometry (MS) to large biomolecules has been revolutionized in the past decade with the development of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) techniques. ESI and MALDI permit solvent evaporation and sublimation of large biomolecules into the gaseous phase, respectively. The coupling of ESI or MALDI to an appropriate mass spectrometer has allowed the determination of accurate molecular mass and the detection of chemical modification at high sensitivity (picomole to femtomole). The interface of mass spectrometry hardware with computers and new extended mass spectrometric methods has resulted in the use of MS for protein sequencing, post-translational modifications, protein conformations (native, denatured, folding intermediates), protein folding/unfolding, and protein-protein or protein-ligand interactions. In this review, applications of MS, particularly ESI-MS and MALDI time-of-flight MS, to food proteins and peptides are described.
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Affiliation(s)
- H F Alomirah
- Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, Montreal, Canada
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12
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Affiliation(s)
- A L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA
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13
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Figeys D, Aebersold R. High sensitivity analysis of proteins and peptides by capillary electrophoresis-tandem mass spectrometry: recent developments in technology and applications. Electrophoresis 1998; 19:885-92. [PMID: 9638934 DOI: 10.1002/elps.1150190603] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Analytical biochemistry, in particular the analysis of regulatory proteins that control biological systems and pathways, is dependent on methods of ever-increasing sensitivity. Capillary electrophoresis (CE) has long been recognized as an ultrasensitive analytical technique. In spite of the high sensitivity, CE has not penetrated protein discovery research as a standard analytical method. In this review article we summarize recent technical developments which have significantly enhanced CE as a tool for the analysis of trace amounts of proteins. Specifically, we review recent advances in the development and application of capillary electrophoresis-mass spectrometry (CE-MS) and on-line analyte concentration techniques, and introduce the emerging field of microfluidics as a front end to mass spectrometry (MS).
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Affiliation(s)
- D Figeys
- Department of Molecular Biotechnology, University of Washington, Seattle, USA.
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14
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Lavanant H, Derrick PJ, Heck AJ, Mellon FA. Analysis of nisin A and some of its variants using Fourier transform ion cyclotron resonance mass spectrometry. Anal Biochem 1998; 255:74-89. [PMID: 9448844 DOI: 10.1006/abio.1997.2441] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The lantibiotic nisin and some of its variants and degradation products have been characterized, using a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer and electrospray ionization. The abundances of all products in the sample (i.e., major component, variants, degradation products, and adducts) have been measured quantitatively. The mass resolution obtained in the electrospray ionisation mass spectra was approximately 100,000 over the measured range. The resulting mass accuracy, better than 0.7 ppm (or within 0.001 Da) allowed the molecular masses and in many cases chemical formulae of most components in the mixture to be identified unambiguously. Additionally, amino acid sequence information on nisin and a variant [nisin + 18 Da] was obtained using sustained off-resonance irradiation collisional activated decomposition (SORI-CAD) of mass-selected precursor ions. Even after introducing collision gas into the mass analyser for the SORI-CAD experiments, the mass accuracy in the fragment ion mass spectra was approximately 5 ppm. It was established that the [nisin + 18 Da] molecule, present as a minor component in the mixture, was a species formed predominantly via hydration of nisin at position 33, i.e., [Ser33]nisin, with a small contribution due to hydration at position 5,[2-hydroxy-Ala5]nisin.
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Affiliation(s)
- H Lavanant
- Institute of Mass Spectrometry, University of Warwick, Coventry, United Kingdom
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15
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Monitoring of Process Impurities in Drugs. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0301-4770(08)60317-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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16
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Abstract
The broad category of antibiotics encompasses some of the most widely prescribed pharmaceuticals in the world. As is the case with any pharmaceutical, an antibiotic must be characterized in terms of its potency or activity, and the presence and quantity of impurities. Additionally, any residue or metabolite that may be present as a result of its use must be monitored. Many capillary electrophoretic techniques have been utilized in the analysis of antibiotics, addressing the various aspects of their quantitation, profiling, and monitoring. Some of the more recent applications are summarized in this review article.
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Affiliation(s)
- C L Flurer
- Forensic Chemistry Center, Food and Drug Administration, Cincinnati, OH 45202, USA
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17
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Cho BY, Strong R, Fate G, Krull IS. High-performance capillary electrophoresis of a fermentation-derived cyclic peptide analog, animal growth promoter. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1997; 697:163-74. [PMID: 9342666 DOI: 10.1016/s0378-4347(97)00285-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have developed HPCE methods for the analysis of sulfomycin (trivial name) and related compounds (code name, crude material = U82127 = I), which is an animal growth promoter derived from a fermentation beer. The crude material, I, isolated from the fermentation consisted of more than 40 components which were not completely separated by conventional HPLC. Thus, as a complementary analysis method, we have optimized HPCE conditions for I using various capillaries including uncoated, coated, and packed using various buffers. The optimized HPCE conditions were obtained with an uncoated fused-silica capillary and a buffer that consisted of 30 mM Tris-tricine, 10 mM SDS, 10 mM NaCl and 20% MeOH, pH 8.0. Using these HPCE conditions, we were able to separate the one main component collected from the HPLC effluent into two or three components. In order to identify the main components of the fermentation product, an off-line HPLC-HPCE-MS analysis for I was performed. From the MALDI-TOF-MS results, the separated components collected from HPCE had different molecular masses. Four lots of I samples having different characteristics were also analyzed by HPCE to investigate lot-to-lot differences in peak profiles. The four lots of I were found to have very similar peak profiles. In this paper, I refers to the crude fermentation product and sulfomycin to the purified, major HPLC component of I.
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Affiliation(s)
- B Y Cho
- Northeastern University, Department of Chemistry, Boston, MA 02115, USA
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