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Zhang J, Gu S, Zhang T, Wu Y, Ma J, Zhao L, Li X, Zhang J. Characterization and antibacterial modes of action of bacteriocins from Bacillus coagulans CGMCC 9951 against Listeria monocytogenes. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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2
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Parisi G, Palopoli N, Tosatto SC, Fornasari MS, Tompa P. "Protein" no longer means what it used to. Curr Res Struct Biol 2021; 3:146-152. [PMID: 34308370 PMCID: PMC8283027 DOI: 10.1016/j.crstbi.2021.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 01/02/2023] Open
Abstract
Every biologist knows that the word protein describes a group of macromolecules essential to sustain life on Earth. As biologists, we are invariably trained under a protein paradigm established since the early twentieth century. However, in recent years, the term protein unveiled itself as an euphemism to describe the overwhelming heterogeneity of these compounds. Most of our current studies are targeted on carefully selected subsets of proteins, but we tend to think and write about these as representative of the whole population. Here we discuss how seeking for universal definitions and general rules in any arbitrarily segmented study would be misleading about the conclusions. Of course, it is not our purpose to discourage the use of the word protein. Instead, we suggest to embrace the extended universe of proteins to reach a deeper understanding of their full potential, realizing that the term encompasses a group of molecules very heterogeneous in terms of size, shape, chemistry and functions, i.e. the term protein no longer means what it used to.
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Affiliation(s)
- Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | | | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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3
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography. Chembiochem 2020; 21:3463-3475. [DOI: 10.1002/cbic.202000315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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Homologous Expression and Characterization of Gassericin T and Gassericin S, a Novel Class IIb Bacteriocin Produced by Lactobacillus gasseri LA327. Appl Environ Microbiol 2019; 85:AEM.02815-18. [PMID: 30610075 DOI: 10.1128/aem.02815-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 12/23/2018] [Indexed: 01/21/2023] Open
Abstract
Lactobacillus gasseri LA327, isolated from the large intestine tissue in humans, is a bacteriocinogenic strain with two kinds of class IIb bacteriocin structural genes, i.e., those for gassericin T (GT) and acidocin LF221A (Acd LF221A). In this study, DNA sequencing of the genes for GT and Acd LF221A from L. gasseri LA327 revealed that the amino acid sequences for GT corresponded with those for GT genes, except for GatK (histidine kinase). However, Acd LF221A genes had analogues which differed in at least one amino acid residue, to encode a class IIb bacteriocin designated gassericin S (GS). The LA327 strain retained antimicrobial activity after the deletion of the GT structural genes (gatAX); however, both GS and GT activities were lost by deletion of the putative ABC transporter gene (gatT). This indicates that the LA327 strain produces GS and GT and that GS secretion is performed via GT genes with the inclusion of gatT Homologous expression using deletion mutants of GS and GT, each containing a single peptide, elucidated that GS (GasAX) and GT (GatAX) showed synergistic activity as class IIb bacteriocins and that no synergistic activity was observed between GS and GT peptides. The molecular mass of GS was estimated to be theoretical ca. 5,400 Da by in situ activity assay after SDS-PAGE, clarifying that GS was actually expressed as an active class IIb bacteriocin. Furthermore, the stability of expressed GS to pH, heat, and protease was determined.IMPORTANCE Bacteriocins are regarded as potential alternatives for antibiotics in the absence of highly resistant bacteria. In particular, two-peptide (class IIb) bacteriocins exhibit the maximum activity through the synergy of two components, and their antimicrobial spectra are known to be relatively wide. However, there are few reports of synergistic activity of class IIb bacteriocins determined by isolation and purification of individual peptides. Our results clarified the interaction of each class IIb component peptide for GT and GS via the construction of homologous mutants, which were not dependent on the purification. These data may contribute to understanding the mechanisms of action by which class IIb bacteriocins exhibit wide antibacterial spectra.
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Rosengren KJ, Daly NL, Harvey PJ, Craik DJ. The self-association of the cyclotide kalata B2 in solution is guided by hydrophobic interactions. Biopolymers 2016; 100:453-60. [PMID: 23893463 DOI: 10.1002/bip.22269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/17/2013] [Accepted: 04/19/2013] [Indexed: 01/28/2023]
Abstract
The cyclotides are a family of small head-to-tail cyclic plant defense proteins. In addition to their cyclic backbone, cyclotides comprise three disulfide bonds in a knotted arrangement, resulting in a highly cross-braced structure that provides exceptional chemical and proteolytic stability. A number of bioactivities have been associated with cyclotides, including insecticidal, antimicrobial, anti-viral and cytotoxic, and these activities are related to an ability to target and disrupt biological membranes. Kalata B2 and to a lesser extent kalata B1, isolated from Oldenlandia affinis, self-associate to tetramers and octamers in aqueous buffers, and this oligomerization has been suggested to be relevant for their ability to form pores in membranes. Here we demonstrate by solution NMR spectroscopy analysis that the oligomerization of kalata B2 is concentration dependent and that it involves the packing of hydrophobic residues normally exposed on the surface of kalata B2 into a multimeric hydrophobic core. Interestingly, the hydrophobic surface that is "quenched" has previously been shown to be responsible for the ability of kalata B2 to insert into membranes. Thus, it seems unlikely that the oligomers observed in aqueous solution are related to any multimeric state present in a membrane environment, and responsible for the formation of pores. The ability to self-associate might alternatively provide a mechanism for preventing self-toxicity when stored at high concentrations in intracellular compartments.
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Affiliation(s)
- K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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6
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Haglund E. Engineering covalent loops in proteins can serve as an on/off switch to regulate threaded topologies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354107. [PMID: 26291088 DOI: 10.1088/0953-8984/27/35/354107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knots in proteins are under active investigation motivating refinements of current techniques and the development of tools to better understand the knotted topology. A strong focus is to identify new knots and expand upon the current understanding of their complex topology. Previous work has shown that the knotted topology, even in the simplest case of knots, encompasses a variety of unique challenges in folding and tying a chain. To bypass many of the in vitro experimental complications involved in working with knots, it is useful to apply methodologies to a more simplified system. The pierced lasso bundles (PLB), we discovered where a single disulphide bridge holds the threaded topology together, presents a simpler system to study knots in vitro. Having a disulphide bridge as an on/off switch between the threaded/unthreaded topology is advantageous because a covalent loop allows manipulation of the knot without directly altering affecting secondary and tertiary structure. Because disulphide bridges are commonly used in protein engineering, a pierced lasso (PL) topology can be easily introduced into a protein of interest to form a knotted topology within a given secondary structure. It is also important to take into account that if formed, disulphides can inadvertently introduce an unwanted PL. This was found upon determination of the crystal structure (PDB code 2YHG) of the recently de novo designed nucleoside hydrolase. Our detailed investigations of the PL presented here will allow researchers to look at the introduction of disulphide bridges in a larger context with respect to potential geometrical consequences on the structure and functional properties of proteins.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California, San Diego (UCSD), La Jolla, CA 92093, USA. Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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7
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Gassericin A: a circular bacteriocin produced by Lactic acid bacteria Lactobacillus gasseri. World J Microbiol Biotechnol 2013; 29:1977-87. [DOI: 10.1007/s11274-013-1368-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/03/2013] [Indexed: 10/26/2022]
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8
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Soengas RG, Fontanella M, Santos JI, Fleet GWJ, Jiménez-Barbero J. Synthesis and Conformational Analysis of Heterogeneous Cyclic Oligomers of 6-Amino-6-deoxygalactonic Acid and Phenylalanine. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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9
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Conlan BF, Colgrave ML, Gillon AD, Guarino R, Craik DJ, Anderson MA. Insights into processing and cyclization events associated with biosynthesis of the cyclic Peptide kalata B1. J Biol Chem 2012; 287:28037-46. [PMID: 22700963 PMCID: PMC3431668 DOI: 10.1074/jbc.m112.347823] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 05/31/2012] [Indexed: 11/06/2022] Open
Abstract
Plant cyclotides are the largest family of gene-encoded cyclic proteins. They act as host defense molecules to protect plants and are promising candidates as insecticidal and nematocidal agents in agriculture. For this promise to be realized a greater understanding of the post-translational processing of these proteins is needed. Cyclotides are cleaved from precursor proteins with subsequent ligation of the N and C termini to form a continuous peptide backbone. This cyclization step is inefficient in transgenic plants and our work aims to shed light on the specificity requirements at the excision sites for cyclic peptide production. Using the prototypic cyclotide kalata B1 (kB1) expressed from the Oak1 gene, MALDI-TOF mass spectrometry was used to examine the cyclization efficiency when mutants of the Oak1 gene were expressed in transgenic Nicotiana benthamiana. Cleavage at the N terminus of the cyclotide domain occurs rapidly with no strict specificity requirements for amino acids at the cleavage site. In contrast, the C-terminal region of the cyclotide domain in the P2, P1, P1', and P2' positions is highly conserved and only specific amino acids can occupy these positions. The cyclization reaction requires an Asn at position P1 followed by a small amino acid (Ala, Gly, Ser) at the P1' position. The P2' position must be filled by Leu or Ile; in their absence an unusual post-translational modification occurs. Substitution of the P2' Leu with Ala leads to hydroxylation of the neighboring proline. Through mutational analysis this novel proline hydroxylation motif was determined to be Gly-Ala-Pro-Ser.
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Affiliation(s)
- Brendon F. Conlan
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
| | | | - Amanda D. Gillon
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
| | - Rosemary Guarino
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
| | - David J. Craik
- the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marilyn A. Anderson
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
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10
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van Lieshout JFT, Gutiérrez ONP, Vroom W, Planas A, de Vos WM, van der Oost J, Koutsopoulos S. Thermal stabilization of an endoglucanase by cyclization. Appl Biochem Biotechnol 2012; 167:2039-53. [PMID: 22653681 PMCID: PMC3416981 DOI: 10.1007/s12010-012-9674-z] [Citation(s) in RCA: 15] [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: 01/17/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
An intein-driven protein splicing approach allowed for the covalent linkage between the N- and C-termini of a polypeptide chain to create circular variants of the endo-β-1,3-1,4-glucanase, LicA, from Bacillus licheniformis. Two circular variants, LicA-C1 and LicA-C2, which have connecting loops of 20 and 14 amino acids, respectively, showed catalytic activities that are approximately two and three times higher, respectively, compared to that of the linear LicA (LicA-L1). The thermal stability of the circular variants was significantly increased compared to the linear form. Whereas the linear glucanase lost half of its activity after 3 min at 65 °C, the two circular variants have 6-fold (LicA-C1) and 16-fold (LicA-C2) increased half-life time of inactivation. In agreement with this, fluorescence spectroscopy and differential scanning calorimetry studies revealed that circular enzymes undergo structural changes at higher temperatures compared to that of the linear form. The effect of calcium on the conformational stability and function of the circular LicAs was also investigated, and we observed that the presence of calcium ions results in increased thermal stability. The impact of the length of the designed loops on thermal stability of the circular proteins is discussed, and it is suggested that cyclization may be an efficient strategy for the increased stability of proteins.
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Affiliation(s)
- Johan F. T. van Lieshout
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Odette N. Pérez Gutiérrez
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Wietse Vroom
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Sotirios Koutsopoulos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
- Center for Biomedical Engineering, NE47-307, Massachusetts Institute of Technology, Cambridge, MA 02139-4307 USA
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11
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Abstract
Circular proteins, once thought to be rare, are now commonly found in plants. Their chemical synthesis, once thought to be difficult, is now readily achievable. The enabling methodology is largely due to the advances in entropic chemical ligation to overcome the entropy barrier in coupling the N- and C-terminal ends of large peptide segments for either intermolecular ligation or intramolecular ligation in end-to-end cyclization. Key elements of an entropic chemical ligation consist of a chemoselective capture step merging the N and C termini as a covalently linked O/S-ester intermediate to permit the subsequent step of an intramolecular O/S-N acyl shift to form an amide. Many ligation methods exploit the supernucleophilicity of a thiol side chain at the N terminus for the capture reaction, which makes cysteine-rich peptides ideal candidates for the entropy-driven macrocyclization. Advances in desulfurization and modification of the thiol-containing amino acids at the ligation sites to other amino acids add extra dimensions to the entropy-driven ligation methods. This minireview describes recent advances of entropy-driven ligation to prepare circular proteins with or without a cysteinyl side chain.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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12
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Jain S, Kahnt J, van der Does C. Processing and maturation of the pilin of the type IV secretion system encoded within the gonococcal genetic island. J Biol Chem 2011; 286:43601-43610. [PMID: 22006923 DOI: 10.1074/jbc.m111.264028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The type IV secretion system (T4SS) encoded within the gonococcal genetic island (GGI) of Neisseria gonorrhoeae has homology to the T4SS encoded on the F plasmid. The GGI encodes the putative pilin protein TraA and a serine protease TrbI, which is homologous to the TraF protein of the RP4 plasmid involved in circularization of pilin subunits of P-type pili. TraA was processed to a 68-amino acid long circular peptide by leader peptidase and TrbI. Processing occurred after co-translational membrane insertion and was independent of other proteins. Circularization occurred after removal of three C-terminal amino acids. Mutational analysis of TraA revealed limited flexibility at the cleavage and joining sites. Mutagenesis of TrbI showed that the conserved Lys-93 and Asp-155 are essential, whereas mutagenesis of Ser-52, the putative catalytic serine did not influence circularization. Further mutagenesis of other serine residues did not identify a catalytic serine, indicating that TrbI either contains redundant catalytic serine residues or does not function via a serine-lysine dyad mechanism. In vitro studies revealed that circularization occurs via a covalent intermediate between the C terminus of TraA and TrbI. The intermediate is processed to the circular form after cleavage of the N-terminal signal sequence. This is the first demonstration of a covalent intermediate in the circularization mechanism of conjugative pili.
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Affiliation(s)
- Samta Jain
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands; Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany
| | - Jörg Kahnt
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany
| | - Chris van der Does
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands; Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., 35043 Marburg, Germany.
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Daly NL, Rosengren KJ, Troeira Henriques S, Craik DJ. NMR and protein structure in drug design: application to cyclotides and conotoxins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:359-70. [DOI: 10.1007/s00249-011-0672-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 12/28/2010] [Accepted: 01/03/2011] [Indexed: 01/14/2023]
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Ireland DC, Clark RJ, Daly NL, Craik DJ. Isolation, sequencing, and structure-activity relationships of cyclotides. JOURNAL OF NATURAL PRODUCTS 2010; 73:1610-1622. [PMID: 20718473 DOI: 10.1021/np1000413] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Cyclotides are a topologically fascinating family of miniproteins discovered over the past decade that have expanded the diversity of plant-derived natural products. They are approximately 30 amino acids in size and occur in plants of the Violaceae, Rubiaceae, and Cucurbitaceae families. Despite their proteinaceous composition, cyclotides behave in much the same way as many nonpeptidic natural products in that they are resistant to degradation by enzymes or heat and can be extracted from plants using methanol. Their stability arises, in large part, due to their characteristic cyclic cystine knot (CCK) structural motif. Cystine knots are present in a variety of proteins of insect, plant, and animal origin, comprising a ring formed by two disulfide bonds and their connecting backbone segments that is threaded by a third disulfide bond. In cyclotides, the cystine knot is uniquely embedded within a head-to-tail cyclized peptide backbone, leading to the ultrastable CCK structural motif. Apart from the six absolutely conserved cysteine residues, the majority of amino acids in the six backbone loops of cyclotides are tolerant to variation. It has been predicted that the family might include up to 50,000 members; although, so far, sequences for only 140 have been reported. Cyclotides exhibit a variety of biological activities, including insecticidal, nematocidal, molluscicidal, antimicrobial, antibarnacle, anti-HIV, and antitumor activities. Due to their diverse activities and common structural core from which variable loops protrude, cyclotides can be thought of as combinatorial peptide templates capable of displaying a variety of amino acid sequences. They have thus attracted interest in drug design as well as in crop protection applications.
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Affiliation(s)
- David C Ireland
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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15
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Conlan BF, Gillon AD, Craik DJ, Anderson MA. Circular proteins and mechanisms of cyclization. Biopolymers 2010; 94:573-83. [DOI: 10.1002/bip.21422] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Comegna D, Benincasa M, Gennaro R, Izzo I, De Riccardis F. Design, synthesis and antimicrobial properties of non-hemolytic cationic alpha-cyclopeptoids. Bioorg Med Chem 2010; 18:2010-8. [PMID: 20153656 DOI: 10.1016/j.bmc.2010.01.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/08/2010] [Accepted: 01/09/2010] [Indexed: 11/19/2022]
Abstract
The synthesis and screening of neutral and cationic, linear and cyclic peptoids (N-alkylglycine peptidomimetics) is described. Structure-activity relationship studies show that the in vitro activities of the tested peptoids depend on both cyclization and decoration with cationic groups. The most powerful N-lysine cyclopeptoid derivatives showed good antifungal activity against Candida albicans (ATCC90029 and L21) and Candida famata (SA550, Amph B-resistant) and low hemolytic activity. The effects of the cyclic peptoids on membrane permeabilization were evaluated by the propidium iodide exclusion assay.
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Affiliation(s)
- Daniela Comegna
- Deparment of Chemistry, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano (SA), Italy
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17
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Cascales L, Craik DJ. Naturally occurring circular proteins: distribution, biosynthesis and evolution. Org Biomol Chem 2010; 8:5035-47. [DOI: 10.1039/c0ob00139b] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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18
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Liang QL, Zhou K, He HX. Retrocyclin 2: a new therapy against avian influenza H5N1 virus in vivo and vitro. Biotechnol Lett 2009; 32:387-92. [DOI: 10.1007/s10529-009-0167-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 01/26/2023]
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19
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Martin-Visscher LA, Gong X, Duszyk M, Vederas JC. The three-dimensional structure of carnocyclin A reveals that many circular bacteriocins share a common structural motif. J Biol Chem 2009; 284:28674-81. [PMID: 19692336 PMCID: PMC2781411 DOI: 10.1074/jbc.m109.036459] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Carnocyclin A (CclA) is a potent antimicrobial peptide from Carnobacterium maltaromaticum UAL307 that displays a broad spectrum of activity against numerous Gram-positive organisms. An amide bond links the N and C termini of this bacteriocin, imparting stability and structural integrity to this 60-amino acid peptide. CclA interacts with lipid bilayers in a voltage-dependent manner and forms anion selective pores. Several other circular bacteriocins have been reported, yet only one (enterocin AS-48) has been structurally characterized. We have now determined the solution structure of CclA by NMR and further examined its anion binding and membrane channel properties. The results reveal that CclA preferentially binds halide anions and has a structure that is surprisingly similar to that of AS-48 despite low sequence identity, different oligomeric state, and disparate function. CclA folds into a compact globular bundle, comprised of four helices surrounding a hydrophobic core. NMR studies show two fluoride ion binding modes for CclA. Our findings suggest that although other circular bacteriocins are likely to have diverse mechanisms of action, many may have a common structural motif. This shared three-dimensional arrangement resembles the fold of mammalian saposins, peptides that either directly lyse membranes or serve as activators of lipid-degrading enzymes.
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Austin J, Kimura RH, Woo YH, Camarero JA. In vivo biosynthesis of an Ala-scan library based on the cyclic peptide SFTI-1. Amino Acids 2009; 38:1313-22. [PMID: 19685144 DOI: 10.1007/s00726-009-0338-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022]
Abstract
We present the in vivo biosynthesis of wild-type sunflower trypsin inhibitor 1 (SFTI-1) inside E. coli cells using an intramolecular native chemical ligation in combination with a modified protein splicing unit. SFTI-1 is a small backbone cyclized polypeptide with a single disulfide bridge. A small library containing multiple Ala mutants was also biosynthesized and its activity was assayed using a trypsin-binding assay. This study clearly demonstrates the exciting possibility of generating large cyclic peptide libraries in live E. coli cells, and is a critical first step for developing in vivo screening and directed evolution technologies using the cyclic peptide SFTI-1 as a molecular scaffold.
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Affiliation(s)
- Jeffrey Austin
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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21
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McIntosh JA, Donia MS, Schmidt EW. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Nat Prod Rep 2009; 26:537-59. [PMID: 19642421 PMCID: PMC2975598 DOI: 10.1039/b714132g] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Ribosomally synthesized bacterial natural products rival the nonribosomal peptides in their structural and functional diversity. The last decade has seen substantial progress in the identification and characterization of biosynthetic pathways leading to ribosomal peptide natural products with new and unusual structural motifs. In some of these cases, the motifs are similar to those found in nonribosomal peptides, and many are constructed by convergent or even paralogous enzymes. Here, we summarize the major structural and biosynthetic categories of ribosomally synthesized bacterial natural products and, where applicable, compare them to their homologs from nonribosomal biosynthesis.
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Affiliation(s)
- John A. McIntosh
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
| | - Mohamed S. Donia
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
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22
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Identification and characterization of lactocyclicin Q, a novel cyclic bacteriocin produced by Lactococcus sp. strain QU 12. Appl Environ Microbiol 2009; 75:1552-8. [PMID: 19139222 DOI: 10.1128/aem.02299-08] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus sp. strain QU 12, which was isolated from cheese, produced a novel cyclic bacteriocin termed lactocyclicin Q. By using cation-exchange chromatography, hydrophobic interaction chromatography, and reverse-phase high-performance liquid chromatography, lactocyclicin Q was purified from culture supernatant, and its molecular mass was determined to be 6,062.8 Da by mass spectrometry. Lactocyclicin Q has been characterized by its unique antimicrobial spectrum, high level of protease resistance, and heat stability compared to other reported bacteriocins of lactic acid bacteria. The amino acid sequence of lactocyclicin Q was determined chemically, and this compound is composed of 61 amino acid residues that have a cyclic structure with linkage between the N and C termini by a peptide bond. It showed no homology to any other antimicrobial peptide, including cyclic bacteriocins. On the basis of the amino acid sequences obtained, the sequence of the gene encoding the prepeptide lactocyclicin Q was obtained. This is the first report of a cyclic bacteriocin purified from a strain belonging to the genus Lactococcus.
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23
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Kleineweischede R, Hackenberger CPR. Chemoselective peptide cyclization by traceless Staudinger ligation. Angew Chem Int Ed Engl 2008; 47:5984-8. [PMID: 18604792 DOI: 10.1002/anie.200801514] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rolf Kleineweischede
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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24
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Knappe TA, Linne U, Zirah S, Rebuffat S, Xie X, Marahiel MA. Isolation and Structural Characterization of Capistruin, a Lasso Peptide Predicted from the Genome Sequence of Burkholderia thailandensis E264. J Am Chem Soc 2008; 130:11446-54. [PMID: 18671394 DOI: 10.1021/ja802966g] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Thomas A. Knappe
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Chimie et Biochimie des Substances Naturelles, UMR 5154 CNRS, Muséum National d’Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Uwe Linne
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Chimie et Biochimie des Substances Naturelles, UMR 5154 CNRS, Muséum National d’Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Séverine Zirah
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Chimie et Biochimie des Substances Naturelles, UMR 5154 CNRS, Muséum National d’Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Sylvie Rebuffat
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Chimie et Biochimie des Substances Naturelles, UMR 5154 CNRS, Muséum National d’Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Xiulan Xie
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Chimie et Biochimie des Substances Naturelles, UMR 5154 CNRS, Muséum National d’Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Mohamed A. Marahiel
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany, and Chimie et Biochimie des Substances Naturelles, UMR 5154 CNRS, Muséum National d’Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
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25
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Martin-Visscher LA, van Belkum MJ, Garneau-Tsodikova S, Whittal RM, Zheng J, McMullen LM, Vederas JC. Isolation and characterization of carnocyclin a, a novel circular bacteriocin produced by Carnobacterium maltaromaticum UAL307. Appl Environ Microbiol 2008; 74:4756-63. [PMID: 18552180 PMCID: PMC2519327 DOI: 10.1128/aem.00817-08] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 06/09/2008] [Indexed: 11/20/2022] Open
Abstract
Carnobacterium maltaromaticum UAL307, isolated from fresh pork, exhibits potent activity against a number of gram-positive organisms, including numerous Listeria species. Three bacteriocins were isolated from culture supernatant, and using matrix-assisted laser desorption ionization-time of flight mass spectrometry and Edman sequencing, two of these bacteriocins were identified as piscicolin 126 and carnobacteriocin BM1, both of which have previously been described. The remaining bacteriocin, with a molecular mass of 5,862 Da, could not be sequenced by traditional methods, suggesting that the peptide was either cyclic or N-terminally blocked. This bacteriocin showed remarkable stability over a wide temperature and pH range and was unaffected by a variety of proteases. After digestion with trypsin and alpha-chymotrypsin, the peptide was de novo sequenced by tandem mass spectrometry and a linear sequence deduced, consisting of 60 amino acids. Based on this sequence, the molecular mass was predicted to be 5,880 Da, 18 units higher than the observed molecular mass, which suggested that the peptide has a cyclic structure. Identification of the genetic sequence revealed that this peptide is circular, formed by a covalent linkage between the N and C termini following cleavage of a 4-residue peptide leader sequence. The results of structural studies suggest that the peptide is highly structured in aqueous conditions. This bacteriocin, named carnocyclin A, is the first reported example of a circular bacteriocin produced by Carnobacterium spp.
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26
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Kleineweischede R, Hackenberger C. Chemoselektive Peptidcyclisierung über spurlose Staudinger-Ligation. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801514] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Colgrave ML, Kotze AC, Huang YH, O’Grady J, Simonsen SM, Craik DJ. Cyclotides: Natural, Circular Plant Peptides that Possess Significant Activity against Gastrointestinal Nematode Parasites of Sheep. Biochemistry 2008; 47:5581-9. [DOI: 10.1021/bi800223y] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michelle L. Colgrave
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia, and CSIRO Division of Livestock Industries, CSIRO, Brisbane 4072, Australia
| | - Andrew C. Kotze
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia, and CSIRO Division of Livestock Industries, CSIRO, Brisbane 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia, and CSIRO Division of Livestock Industries, CSIRO, Brisbane 4072, Australia
| | - John O’Grady
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia, and CSIRO Division of Livestock Industries, CSIRO, Brisbane 4072, Australia
| | - Shane M. Simonsen
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia, and CSIRO Division of Livestock Industries, CSIRO, Brisbane 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia, and CSIRO Division of Livestock Industries, CSIRO, Brisbane 4072, Australia
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28
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Maqueda M, Sánchez-Hidalgo M, Fernández M, Montalbán-López M, Valdivia E, Martínez-Bueno M. Genetic features of circular bacteriocins produced by Gram-positive bacteria. FEMS Microbiol Rev 2008; 32:2-22. [DOI: 10.1111/j.1574-6976.2007.00087.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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29
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Duquesne S, Destoumieux-Garzón D, Zirah S, Goulard C, Peduzzi J, Rebuffat S. Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli. ACTA ACUST UNITED AC 2007; 14:793-803. [PMID: 17656316 DOI: 10.1016/j.chembiol.2007.06.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/01/2007] [Accepted: 06/05/2007] [Indexed: 11/22/2022]
Abstract
Microcin J25 (MccJ25) is a gene-encoded lasso peptide secreted by Escherichia coli which exerts a potent antibacterial activity by blocking RNA polymerase. Here we demonstrate that McjB and McjC, encoded by genes in the MccJ25 gene cluster, catalyze the maturation of MccJ25. Requirement for both McjB and McjC was shown by gene inactivation and complementation assays. Furthermore, the conversion of the linear precursor McjA into mature MccJ25 was obtained in vitro in the presence of McjB and McjC, all proteins being produced by recombinant expression in E. coli. Analysis of the amino acid sequences revealed that McjB could possess proteolytic activity, whereas McjC would be the ATP/Mg(2+)-dependent enzyme responsible for the formation of the Gly1-Glu8 amide bond. Finally, we show that putative lasso peptides are widespread among Proteobacteria and Actinobacteria.
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Affiliation(s)
- Sophie Duquesne
- Chimie et Biochimie des Substances Naturelles, UMR 5154 CNRS, Muséum National d'Histoire Naturelle, CP 54, 57 rue Cuvier, 75005 Paris, France
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30
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Wirawan RE, Swanson KM, Kleffmann T, Jack RW, Tagg JR. Uberolysin: a novel cyclic bacteriocin produced by Streptococcus uberis. MICROBIOLOGY-SGM 2007; 153:1619-1630. [PMID: 17464077 DOI: 10.1099/mic.0.2006/005967-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptococcus uberis is commonly found in the environment and in association with various bovine body sites and is a major cause of bovine mastitis. Moreover, S. uberis is known to produce a variety of bacteriocin-like inhibitory substances, antimicrobial agents that generally inhibit closely related bacterial species. In this respect, S. uberis strain 42 has previously been shown to produce a novel nisin variant named nisin U. This paper reports that, in addition to nisin U, S. uberis strain 42 produces a second bacteriocin that induces the lysis of metabolically active, susceptible target bacteria and which has therefore been named uberolysin. Isolation of the native active antimicrobial agent revealed that uberolysin is a 7048 Da peptide that is refractory to sequence analysis by Edman degradation. Transposon mutagenesis was used to generate a uberolysin-negative mutant of S. uberis 42 and sequencing of DNA flanking the insertion site revealed, in addition to the structural gene (ublA), several open reading frames likely to be involved in post-translational modification, transport and producer self-protection (immunity), and possibly in regulation of the biosynthetic gene cluster. In addition, a pair of direct repeats that may be involved in bacteriocin acquisition were identified; indeed, ublA could be identified in 18 % of tested S. uberis strains. Enzymic hydrolysis of uberolysin was used to confirm that ublA does indeed encode the precursor of uberolysin, that an unusually short leader sequence of only six amino acids is cleaved during processing of the mature peptide and that uberolysin is post-translationally covalently modified to form a head-to-tail monocycle. Thus, uberolysin is a unique cyclic bacteriocin, belonging to the same family of bacteriocins as enterocin AS-48 and circularin A.
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Affiliation(s)
- Ruth E Wirawan
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Kara M Swanson
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Torsten Kleffmann
- Centre for Protein Research (Department of Biochemistry), Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Ralph W Jack
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
| | - John R Tagg
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, PO Box 56, Dunedin, New Zealand
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31
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Craik DJ, Daly NL. NMR as a tool for elucidating the structures of circular and knotted proteins. MOLECULAR BIOSYSTEMS 2007; 3:257-65. [PMID: 17372654 DOI: 10.1039/b616856f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclotides are a recently discovered family of mini-proteins that have a head-to-tail cyclised backbone stabilized by a knotted arrangement of three disulfide bonds. They have a wide range of biological activities, including uterotonic, anti-bacterial, anti-HIV, and anti-tumour activity but their insecticidal activities suggest that their natural function is in plant defense. They are exceptionally resistant to chemical, enzymatic and thermal treatments because of their unique structural scaffold. This stability and resistance to proteolysis makes them a potentially valuable protein engineering tool at the interface of chemistry and biology: they have the structure of proteins but the stability and biophysical properties of organic molecules. In this review the role of NMR in defining the structures of cyclotides is described.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience and Australian Research Council Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane QLD 4072, Australia.
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32
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Synthetic Approaches to Disulfide-free Circular Bovine Pancreatic Trypsin Inhibitor (c-BPTI) Analogues. Int J Pept Res Ther 2006. [DOI: 10.1007/s10989-006-9023-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Ireland DC, Colgrave ML, Nguyencong P, Daly NL, Craik DJ. Discovery and Characterization of a Linear Cyclotide from Viola odorata: Implications for the Processing of Circular Proteins. J Mol Biol 2006; 357:1522-35. [PMID: 16488428 DOI: 10.1016/j.jmb.2006.01.051] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 01/11/2006] [Accepted: 01/12/2006] [Indexed: 10/25/2022]
Abstract
Cyclotides are mini-proteins of 28-37 amino acid residues that have the unusual feature of a head-to-tail cyclic backbone surrounding a cystine knot. This molecular architecture gives the cyclotides heightened resistance to thermal, chemical and enzymatic degradation and has prompted investigations into their use as scaffolds in peptide therapeutics. There are now more than 80 reported cyclotide sequences from plants in the families Rubiaceae, Violaceae and Cucurbitaceae, with a wide variety of biological activities observed. However, potentially limiting the development of cyclotide-based therapeutics is a lack of understanding of the mechanism by which these peptides are cyclized in vivo. Until now, no linear versions of cyclotides have been reported, limiting our understanding of the cyclization mechanism. This study reports the discovery of a naturally occurring linear cyclotide, violacin A, from the plant Viola odorata and discusses the implications for in vivo cyclization of peptides. The elucidation of the cDNA clone of violacin A revealed a point mutation that introduces a stop codon, which inhibits the translation of a key Asn residue that is thought to be required for cyclization. The three-dimensional solution structure of violacin A was determined and found to adopt the cystine knot fold of native cyclotides. Enzymatic stability assays on violacin A indicate that despite an increase in the flexibility of the structure relative to cyclic counterparts, the cystine knot preserves the overall stability of the molecule.
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Affiliation(s)
- David C Ireland
- Institute for Molecular Bioscience and Australian Research Council Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane, Qld 4072, Australia
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34
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Simonsen SM, Sando L, Ireland DC, Colgrave ML, Bharathi R, Göransson U, Craik DJ. A continent of plant defense peptide diversity: cyclotides in Australian Hybanthus (Violaceae). THE PLANT CELL 2005; 17:3176-89. [PMID: 16199617 PMCID: PMC1276036 DOI: 10.1105/tpc.105.034678] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cyclotides are plant-derived miniproteins that have the unusual features of a head-to-tail cyclized peptide backbone and a knotted arrangement of disulfide bonds. It had been postulated that they might be an especially large family of host defense agents, but this had not yet been tested by field data on cyclotide variation in wild plant populations. In this study, we sampled Australian Hybanthus (Violaceae) to gain an insight into the level of variation within populations, within species, and between species. A wealth of cyclotide diversity was discovered: at least 246 new cyclotides are present in the 11 species sampled, and 26 novel sequences were characterized. A new approach to the discovery of cyclotide sequences was developed based on the identification of a conserved sequence within a signal sequence in cyclotide precursors. The number of cyclotides in the Violaceae is now estimated to be >9000. Cyclotide physicochemical profiles were shown to be a useful taxonomic feature that reflected species and their morphological relationships. The novel sequences provided substantial insight into the tolerance of the cystine knot framework in cyclotides to amino acid substitutions and will facilitate protein engineering applications of this framework.
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Affiliation(s)
- Shane M Simonsen
- Institute for Molecular Bioscience, University of Queensland, Australian Research Council Special Research Centre for Functional and Applied Genomics, Brisbane 4072, Australia
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35
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Rosengren KJ, Göransson U, Otvos L, Craik DJ. Cyclization of pyrrhocoricin retains structural elements crucial for the antimicrobial activity of the native peptide. Biopolymers 2004; 76:446-58. [PMID: 15478127 DOI: 10.1002/bip.20159] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pyrrhocoricin is a naturally occurring antimicrobial peptide from the European fire bug Pyrrhocoris apterus. It has submicromolar activity against a range of Gram-negative bacterial strains and has created recent interest as a lead for the development of novel antibiotic compounds. In this study, we have used NMR spectroscopy to determine the solution structures of pyrrhocoricin and a synthetic macrocyclic derivative that has improved in vivo pharmaceutical properties. Native pyrrhocoricin is largely disordered in solution, but there is evidence of a subpopulation with ordered turn regions over residues 2-5, 4-7, and 16-19. The macrocyclic derivative incorporates a nine amino acid linker joining the N- and C-termini, which does not adversely affect the antimicrobial potency but leads to a broader spectrum of activity. The NMR data suggest that the turn conformations in the cyclic derivative are similar to those in the native form, thus implicating them in the biological function.
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Affiliation(s)
- K Johan Rosengren
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
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36
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Daly NL, Gustafson KR, Craik DJ. The role of the cyclic peptide backbone in the anti-HIV activity of the cyclotide kalata B1. FEBS Lett 2004; 574:69-72. [PMID: 15358541 DOI: 10.1016/j.febslet.2004.08.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 07/23/2004] [Accepted: 08/06/2004] [Indexed: 11/26/2022]
Abstract
The plant cyclotides, the largest known family of circular proteins, have tightly folded structures and a range of biological activities that lend themselves to potential pharmaceutical and agricultural applications. Based on sequence homology, they are classified into the bracelet and Möbius subfamilies. The bracelet subfamily has previously been shown to display anti-HIV activity. We show here that a member of the Möbius subfamily, kalata B1, also exhibits anti-HIV activity despite extensive sequence differences between the subfamilies. In addition, acyclic permutants of kalata B1 displayed no anti-HIV activity, suggesting that this activity is critically dependent on an intact circular backbone.
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Affiliation(s)
- Norelle L Daly
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
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37
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Yasin B, Wang W, Pang M, Cheshenko N, Hong T, Waring AJ, Herold BC, Wagar EA, Lehrer RI. Theta defensins protect cells from infection by herpes simplex virus by inhibiting viral adhesion and entry. J Virol 2004; 78:5147-56. [PMID: 15113897 PMCID: PMC400355 DOI: 10.1128/jvi.78.10.5147-5156.2004] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We tested the ability of 20 synthetic theta defensins to protect cells from infection by type 1 and type 2 herpes simplex viruses (HSV-1 and -2, respectively). The peptides included rhesus theta defensins (RTDs) 1 to 3, originally isolated from rhesus macaque leukocytes, and three peptides (retrocyclins 1 to 3) whose sequences were inferred from human theta-defensin (DEFT) pseudogenes. We also tested 14 retrocyclin analogues, including the retro, enantio, and retroenantio forms of retrocyclin 1. Retrocyclins 1 and 2 and RTD 3 protected cervical epithelial cells from infection by both HSV serotypes, but only retrocyclin 2 did so without causing cytotoxicity or requiring preincubation with the virus. Surface plasmon resonance studies revealed that retrocyclin 2 bound to immobilized HSV-2 glycoprotein B (gB2) with high affinity (K(d), 13.3 nM) and that it did not bind to enzymatically deglycosylated gB2. Temperature shift experiments indicated that retrocyclin 2 and human alpha defensins human neutrophil peptide 1 (HNP 1) to HNP 3 protected human cells from HSV-2 by different mechanisms. Retrocyclin 2 blocked viral attachment, and its addition during the binding or penetration phases of HSV-2 infection markedly diminished nuclear translocation of VP16 and expression of ICP4. In contrast, HNPs 1 to 3 had little effect on binding but reduced both VP16 transport and ICP4 expression if added during the postbinding (penetration) period. We recently reported that theta defensins are miniature lectins that bind gp120 of human immunodeficiency virus type 1 (HIV-1) with high affinity and inhibit the entry of R5 and X4 isolates of HIV-1. Given its small size (18 residues), minimal cytotoxicity, lack of activity against vaginal lactobacilli, and effectiveness against both HSV-2 and HIV-1, retrocyclin 2 provides an intriguing prototype for future topical microbicide development.
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Affiliation(s)
- Bushra Yasin
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1731, USA
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38
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Mayes BA, Stetz RJ, Watterson MP, Edwards AA, Ansell CW, Tranter GE, Fleet GW. Towards hydroxylated nylon 6: linear and cyclic oligomers from a protected 6-amino-6-deoxy-d-galactonate––a novel class of carbopeptoid-cyclodextrin (CPCD). ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2003.12.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Sieber SA, Marahiel MA. Learning from nature's drug factories: nonribosomal synthesis of macrocyclic peptides. J Bacteriol 2004; 185:7036-43. [PMID: 14645262 PMCID: PMC296262 DOI: 10.1128/jb.185.24.7036-7043.2003] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Stephan A Sieber
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, 35032 Marburg, Germany
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40
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Huge (14-, 21-, 28-, 35-, 56- and 70-membered ring) macrocyclic lactams––a novel family of carbopeptoid-cyclodextrins. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2003.10.103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Rosengren KJ, Clark RJ, Daly NL, Göransson U, Jones A, Craik DJ. Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone. J Am Chem Soc 2003; 125:12464-74. [PMID: 14531690 DOI: 10.1021/ja0367703] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microcin J25 is a 21 amino acid bacterial peptide that has potent antibacterial activity against Gram-negative bacteria, resulting from its interaction with RNA polymerase. The peptide was previously proposed to have a head-to-tail cyclized peptide backbone and a tight globular structure (Blond, A., Péduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthélémy, M., Prigent, Y., Salomón, R. A., Farías, R. N., Moreno, F. & Rebuffat, S. Eur. J. Biochem. 1999, 259, 747-755). It exhibits remarkable thermal stability for a peptide of its size lacking disulfide bonds and in part this was previously proposed to derive from its macrocyclic structure. We show here that in fact the peptide does not have a head-to-tail cyclic structure but rather a side chain to backbone cyclization between Glu8 and the N-terminus. This creates an embedded ring that is threaded by the C-terminal tail of the molecule, forming a noose-like feature. The three-dimensional structure deduced from NMR data suggests that slippage of the noose is prevented by two aromatic residues flanking the embedded ring. Unthreading does not occur even when the molecule is enzymatically digested with thermolysin. The new structural interpretation fully accounts for previously reported NMR and biophysical data and is consistent with the remarkable stability of this potent antimicrobial peptide.
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Affiliation(s)
- K Johan Rosengren
- Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
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