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Agrawal S, Adholeya A, Deshmukh SK. The Pharmacological Potential of Non-ribosomal Peptides from Marine Sponge and Tunicates. Front Pharmacol 2016; 7:333. [PMID: 27826240 PMCID: PMC5078478 DOI: 10.3389/fphar.2016.00333] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/07/2016] [Indexed: 12/18/2022] Open
Abstract
Marine biodiversity is recognized by a wide and unique array of fascinating structures. The complex associations of marine microorganisms, especially with sponges, bryozoans, and tunicates, make it extremely difficult to define the biosynthetic source of marine natural products or to deduce their ecological significance. Marine sponges and tunicates are important source of novel compounds for drug discovery and development. Majority of these compounds are nitrogen containing and belong to non-ribosomal peptide (NRPs) or mixed polyketide-NRP natural products. Several of these peptides are currently under trial for developing new drugs against various disease areas, including inflammatory, cancer, neurodegenerative disorders, and infectious disease. This review features pharmacologically active NRPs from marine sponge and tunicates based on their biological activities.
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Affiliation(s)
| | | | - Sunil K. Deshmukh
- TERI–Deakin Nano Biotechnology Centre, The Energy and Resources InstituteNew Delhi, India
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2
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Craik DJ, Malik U. Cyclotide biosynthesis. Curr Opin Chem Biol 2013; 17:546-54. [PMID: 23809361 DOI: 10.1016/j.cbpa.2013.05.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Cyclotides are bioactive macrocyclic peptides from plants that are characterized by their exceptional stability and potential applications as protein engineering or drug design frameworks. Their stability arises from their unique cyclic cystine knot structure, which combines a head-to-tail cyclic peptide backbone with three conserved disulfide bonds having a knotted topology. Cyclotides are ribosomally synthesized by plants and expressed in a wide range of tissues, including leaves, flowers, stems and roots. Here we describe recent studies that have examined the biosynthesis of cyclotides and in particular the mechanism associated with post-translational backbone cyclization.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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3
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Baindara P, Mandal SM, Chawla N, Singh PK, Pinnaka AK, Korpole S. Characterization of two antimicrobial peptides produced by a halotolerant Bacillus subtilis strain SK.DU.4 isolated from a rhizosphere soil sample. AMB Express 2013; 3:2. [PMID: 23289832 PMCID: PMC3549917 DOI: 10.1186/2191-0855-3-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 01/02/2013] [Indexed: 11/10/2022] Open
Abstract
A bacterial strain producing two antimicrobial peptides was isolated from a rhizosphere soil sample and identified as Bacillus subtilis based on both phenotypic and 16S rRNA gene sequence phylogenetic analysis. It grew optimally up to 14% NaCl and produced antimicrobial peptide within 24 h of growth. The peptides were purified using a combination of chemical extraction and chromatographic techniques. The MALDI-TOF analysis of HPLC purified fractions revealed that the strain SK.DU.4 secreted a bacteriocin-like peptide with molecular mass of 5323.9 Da and a surface-active lipopeptide (m/z 1056 Da). The peptide mass fingerprinting of low-molecular-weight bacteriocin exhibited significant similarity with stretches of secreted lipoprotein of Methylomicrobium album BG8 and displayed 70% sequence coverage. MALDI MS/MS analysis elucidated the lipopeptide as a cyclic lipopeptide with a β-hydroxy fatty acid linked to Ser of a peptide with seven α-amino acids (Asp-Tyr-Asn-Gln-Pro-Asn-Ser) and assigned it to iturin-like group of antimicrobial biosurfactants. However, it differed in amino acid composition with other members of the iturin family. Both peptides were active against Gram-positive bacteria, suggesting that they had an additive effect.
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Affiliation(s)
- Piyush Baindara
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Niharika Chawla
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Pradip Kumar Singh
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Anil Kumar Pinnaka
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Suresh Korpole
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
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Increased penicillin production in Penicillium chrysogenum production strains via balanced overexpression of isopenicillin N acyltransferase. Appl Environ Microbiol 2012; 78:7107-13. [PMID: 22865068 DOI: 10.1128/aem.01529-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intense classical strain improvement has yielded industrial Penicillium chrysogenum strains that produce high titers of penicillin. These strains contain multiple copies of the penicillin biosynthesis cluster encoding the three key enzymes: δ-(l-α-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS), isopenicillin N synthase (IPNS), and isopenicillin N acyltransferase (IAT). The phenylacetic acid coenzyme A (CoA) ligase (PCL) gene encoding the enzyme responsible for the activation of the side chain precursor phenylacetic acid is localized elsewhere in the genome in a single copy. Since the protein level of IAT already saturates at low cluster copy numbers, IAT might catalyze a limiting step in high-yielding strains. Here, we show that penicillin production in high-yielding strains can be further improved by the overexpression of IAT while at very high levels of IAT the precursor 6-aminopenicillic acid (6-APA) accumulates. Overproduction of PCL only marginally stimulates penicillin production. These data demonstrate that in high-yielding strains IAT is the limiting factor and that this limitation can be alleviated by a balanced overproduction of this enzyme.
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Zhang H, Boghigian BA, Armando J, Pfeifer BA. Methods and options for the heterologous production of complex natural products. Nat Prod Rep 2011; 28:125-51. [PMID: 21060956 PMCID: PMC9896020 DOI: 10.1039/c0np00037j] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review will detail the motivations, experimental approaches, and growing list of successful cases associated with the heterologous production of complex natural products.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, Medford, MA 02155, USA.
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Wang Y, Niu L, Li Y, Mao X, Yang Y, Wang C. Single molecule studies of cyclic peptides using molecular matrix at liquid/solid interface by scanning tunneling microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:16305-16311. [PMID: 20593799 DOI: 10.1021/la101467s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We report in this work the single molecule studies of cyclic peptide, cyclosporine A (CsA), using a molecular network formed by star-shaped oligofluorene (StOF-COOH(3)) at the liquid/solid interface by scanning tunneling microscopy (STM). Individual cyclosporine A can be identified and resolved in the molecular network, and the high-resolution STM images of CsA show polygon-like characteristics with a diameter of approximately 1.7 nm. Furthermore, the complex of CsA and Mg(2+) has also been observed to adsorb inside of the molecular matrix. The STM results reveal two adsorption characteristics for the CsA-Mg(2+) complex, which is suggestive of asymmetrical configurations of the complex. The difference in binding energy between the two observed adsorption configurations is estimated to be 1.88 kJ·mol(-1). These results help set the stage for studying the fine structures and functions of various cyclic peptides at the liquid/solid interface.
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Affiliation(s)
- Yibing Wang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
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Post-translational enzyme modification by the phosphopantetheinyl transferase is required for lysine and penicillin biosynthesis but not for roquefortine or fatty acid formation in Penicillium chrysogenum. Biochem J 2008; 415:317-24. [DOI: 10.1042/bj20080369] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NRPSs (non-ribosomal peptide synthetases) and PKSs (polyketide synthases) require post-translational phosphopantetheinylation to become active. This reaction is catalysed by a PPTase (4′-phosphopantetheinyl transferase). The ppt gene of Penicillium chrysogenum, encoding a protein that shares 50% similarity with the stand-alone large PPTases, has been cloned. This gene is present as a single copy in the genome of the wild-type and high-penicillin-producing strains (containing multiple copies of the penicillin gene cluster). Amplification of the ppt gene produced increases in isopenicillin N and benzylpenicillin biosynthesis. A PPTase-defective mutant (Wis54-PPT−) was obtained. It required lysine and lacked pigment and penicillin production, but it still synthesized normal levels of roquefortine. The biosynthesis of roquefortine does not appear to involve PPTase-mediated modification of the synthesizing enzymes. The PPT− mutant did not require fatty acids, which indicates that activation of the fatty acid synthase is performed by a different PPTase. Complementation of Wis54-PPT− with the ppt gene restored lysine biosynthesis, pigmentation and penicillin production, which demonstrates the wide range of processes controlled by this gene.
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Rossbach S, Wilson TL, Kukuk ML, Carty HA. Elevated zinc induces siderophore biosynthesis genes and a zntA-like gene in Pseudomonas fluorescens. FEMS Microbiol Lett 2000; 191:61-70. [PMID: 11004401 DOI: 10.1111/j.1574-6968.2000.tb09320.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Zinc-regulated genes were analyzed in Pseudomonas fluorescens employing mutagenesis with a reporter gene transposon. Six mutants responded with increased gene expression to elevated concentrations of zinc. Genetic and biochemical analysis revealed that in four of the six mutants the transposon had inserted into genes essential for the biosynthesis of the siderophore pyoverdine. The growth of one of the mutants was severely impaired in the presence of elevated concentrations of cadmium and zinc ions. In this mutant, the transposon had inserted in a gene with high similarity to P-type ATPases involved in zinc and cadmium ion transport. Four mutants reacted with reduced gene expression to elevated concentrations of zinc. One of these mutants was sensitive to zinc, cadmium and copper ions. The genetic region targeted in this mutant did not show similarity to any known gene.
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Affiliation(s)
- S Rossbach
- Department of Biological Sciences, Western Michigan University, 1201 Oliver Street, Kalamazoo, MI 49008, USA.
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von Döhren H, Keller U, Vater J, Zocher R. Multifunctional Peptide Synthetases. Chem Rev 1997; 97:2675-2706. [PMID: 11851477 DOI: 10.1021/cr9600262] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hans von Döhren
- Section Biochemistry and Molecular Biology, Max-Volmer-Institute of Biophysical Chemistry and Biochemistry, Technical University Berlin, Franklinstrasse 29, D-10587 Berlin, Germany
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Wessels P, von Döhren H, Kleinkauf H. Biosynthesis of acylpeptidolactones of the daptomycin type. A comparative analysis of peptide synthetases forming A21978C and A54145. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:665-73. [PMID: 9022695 DOI: 10.1111/j.1432-1033.1996.0665r.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A21978C and A54145 are antibacterial 13-residue peptides with a medium-chain-acylated amino terminus and a 10-residue lactone ring; they are produced by strains of Streptomyces roseosporus and Streptomyces fradiae, respectively. The structural differences in their peptide chains, which include amino acid replacements and modifications (L-Glu2-->L-Asn, L-Asn(OH)3-->L-Asp, Sar5-->Gly, L-Ala6-->L-Orn, L-Lys8-->D-Ala, L-Asp(OMe)9-->L-Asp, L-Asn11-->D-Ser, and L-lle13-->L-Kyn; Sar = sarcosine; L-Orn = L-ornithine, L-Kyn = L-kynurenine), reside in the multienzymatic templates directing their biosynthesis. We have examined the peptide synthetases employing immunodetection and substrate activation detected by the amino-acid-dependent ATP-PP1-exchange reaction. Two different antibodies specific for actinomycin synthetase 2 and a peptide sequence characteristic of acyl-CoA-synthetases/peptide synthetases were applied. For the A21978 system two peptide synthetases of 670 and 240 kDa were detected, together with two similar proteins of 630 and 440 kDa occurring in varying amounts. The latter are suggested to be degradation products of an unstable multienzyme. Activation of L-Asp, L-Thr, Gly, L-Orn, L-Ala and L-Ser were assigned to the high-molecular-mass components of 670, 630 and 440 kDa. The 240-kDa protein was purified to homogeneity and shown to catalyse activation of L-kynurenine. The A54145 system consisted of three peptide synthetases of 690, 590 and 250 kDa. Activations of L-Asn. L-Thr and Gly were found. The 250-kDa synthetase was capable of activating isoleucine and valine. Both systems thus show a comparable organisation; implications for the modular construction of their peptide synthetases are discussed.
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Affiliation(s)
- P Wessels
- Institut für Biochemie und Molekulare Biologie, Technische Universität Berlin, Germany
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Affiliation(s)
- J Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Kleinkauf H, Von Döhren H. A nonribosomal system of peptide biosynthesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 236:335-51. [PMID: 8612601 DOI: 10.1111/j.1432-1033.1996.00335.x] [Citation(s) in RCA: 267] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review covers peptide structures originating from the concerted action of enzyme systems without the direct participation of nucleic acids. Biosynthesis proceeds by formation of linear peptidyl intermediates which may be enzymatically modified as well as transformed into specific cyclic structures. The respective enzyme systems are constructed of biosynthetic modules integrated into multienzyme structures. Genetic and DNA-sequence analysis of biosynthetic gene clusters have revealed extensive similarities between prokaryotic and eukaryotic systems, conserved principles of organisation, and a unique mechanism of transport of intermediates during elongation and modification steps involving 4'-phospho-pantetheine. These similarities permit the identification of peptide synthetases and related aminoacyl-ligases and acyl-ligases from sequence data. Similarities to other biosynthetic systems involved in the assembly of polyketide metabolites are discussed.
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Affiliation(s)
- H Kleinkauf
- Institute of Biochemistry and Molecular Biology, Technical University Berlin, Germany
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