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Šink R, Kotnik M, Zega A, Barreteau H, Gobec S, Blanot D, Dessen A, Contreras-Martel C. Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited. PLoS One 2016; 11:e0152075. [PMID: 27031227 PMCID: PMC4816537 DOI: 10.1371/journal.pone.0152075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/08/2016] [Indexed: 11/30/2022] Open
Abstract
The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.
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Affiliation(s)
- Roman Šink
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Miha Kotnik
- Lek Pharmaceuticals d. d., Verovškova 57, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Didier Blanot
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Andréa Dessen
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil
| | - Carlos Contreras-Martel
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- * E-mail:
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52
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Castellano I, Migliaccio O, D’Aniello S, Merlino A, Napolitano A, Palumbo A. Shedding light on ovothiol biosynthesis in marine metazoans. Sci Rep 2016; 6:21506. [PMID: 26916575 PMCID: PMC4768315 DOI: 10.1038/srep21506] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/26/2016] [Indexed: 01/23/2023] Open
Abstract
Ovothiol, isolated from marine invertebrate eggs, is considered one of the most powerful antioxidant with potential for drug development. However, its biological functions in marine organisms still represent a matter of debate. In sea urchins, the most accepted view is that ovothiol protects the eggs by the high oxidative burst at fertilization. In this work we address the role of ovothiol during sea urchin development to give new insights on ovothiol biosynthesis in metazoans. The gene involved in ovothiol biosynthesis OvoA was identified in Paracentrotus lividus genome (PlOvoA). PlOvoA embryo expression significantly increased at the pluteus stage and was up-regulated by metals at concentrations mimicking polluted sea-water and by cyclic toxic algal blooms, leading to ovothiol biosynthesis. In silico analyses of the PlOvoA upstream region revealed metal and stress responsive elements. Structural protein models highlighted conserved active site residues likely responsible for ovothiol biosynthesis. Phylogenetic analyses indicated that OvoA evolved in most marine metazoans and was lost in bony vertebrates during the transition from the aquatic to terrestrial environment. These results highlight the crucial role of OvoA in protecting embryos released in seawater from environmental cues, thus allowing the survival under different conditions.
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Affiliation(s)
- Immacolata Castellano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Oriana Migliaccio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples “Federico II”, Italy
| | | | - Anna Palumbo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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53
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Ishikawa F, Kakeya H. Affinity Purification Method for the Identification of Nonribosomal Peptide Biosynthetic Enzymes Using a Synthetic Probe for Adenylation Domains. Methods Mol Biol 2016; 1401:63-76. [PMID: 26831701 DOI: 10.1007/978-1-4939-3375-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A series of inhibitors have been designed based on 5'-O-sulfamoyl adenosine (AMS) that display tight binding characteristics towards the inhibition of adenylation (A) domains in nonribosomal peptide synthetases (NRPSs). We recently developed an affinity probe for A domains that could be used to facilitate the specific isolation and identification of NRPS modules. Our synthetic probe, which is a biotinylated variant of L-Phe-AMS (L-Phe-AMS-biotin), selectively targets the A domains in NRPS modules that recognize and convert L-Phe to an aminoacyl adenylate in whole proteomes. In this chapter, we describe the design and synthesis of L-Phe-AMS-biotin and provide a summary of our work towards the development of a series of protocols for the specific enrichment of NRPS modules using this probe.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
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54
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Duckworth BP, Wilson DJ, Aldrich CC. Measurement of Nonribosomal Peptide Synthetase Adenylation Domain Activity Using a Continuous Hydroxylamine Release Assay. Methods Mol Biol 2016; 1401:53-61. [PMID: 26831700 PMCID: PMC5588023 DOI: 10.1007/978-1-4939-3375-4_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Adenylation is a crucial enzymatic process in the biosynthesis of nonribosomal peptide synthetase (NRPS) derived natural products. Adenylation domains are considered the gatekeepers of NRPSs since they select, activate, and load the carboxylic acid substrate onto a downstream peptidyl carrier protein (PCP) domain of the NRPS. We describe a coupled continuous kinetic assay for NRPS adenylation domains that substitutes the PCP domain with hydroxylamine as the acceptor molecule. The pyrophosphate released from the first-half reaction is then measured using a two-enzyme coupling system, which detects conversion of the chromogenic substrate 7-methylthioguanosine (MesG) to 7-methylthioguanine. From profiling substrate specificity of unknown or engineered adenylation domains to studying chemical inhibition of adenylating enzymes, this robust assay will be of widespread utility in the broad field NRPS enzymology.
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Affiliation(s)
- Benjamin P Duckworth
- Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
| | - Daniel J Wilson
- Center for Drug Design, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
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55
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Abstract
Filamentous fungi are historically known as rich sources for production of biologically active natural products, so-called secondary metabolites. One particularly pharmaceutically relevant chemical group of secondary metabolites is the nonribosomal peptides synthesized by nonribosomal peptide synthetases (NRPSs). As most of the fungal NRPS gene clusters leading to production of the desired molecules are not expressed under laboratory conditions, efforts to overcome this impediment are crucial to unlock the full chemical potential of each fungal species. One way to activate these silent clusters is by overexpressing and deleting global regulators of secondary metabolism. The conserved fungal-specific regulator of secondary metabolism, LaeA, was shown to be a valuable target for sleuthing of novel gene clusters and metabolites. Additionally, modulation of chromatin structures by either chemical or genetic manipulation has been shown to activate cryptic metabolites. Furthermore, NRPS-derived molecules seem to be affected by cross talk between the specific gene clusters and some of these metabolites have a tissue- or developmental-specific regulation. This chapter summarizes how this knowledge of different tiers of regulation can be combined to increase production of NRPS-derived metabolites in fungal species.
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Affiliation(s)
- Alexandra A Soukup
- Department of Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA
| | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA.
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 3455 Microbial Sciences, 1550 Linden Drive, Madison, WI, 53706, USA.
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 3455 Microbial Sciences, 1550 Linden Drive, Madison, WI, 53706, USA
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56
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Abstract
Bioinformatic sequence analysis allows the functional characterization of newly sequenced proteins. Nonribosomal peptide synthetases (NRPSs) are multi-modular enzymes involved in the biosynthesis of natural products. The current omics era has enabled the exponential growth of the sequenced NRPS, and it is important to characterize the final product of these synthetases. Here, how to achieve the prediction of substrates which bind to adenylation domains in NRPS with NRPSsp (www.nrpssp.com) bioinformatic tool is described.
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Affiliation(s)
- Carlos Prieto
- Bioinformatics Service, Nucleus, University of Salamanca (USAL), Edificio I+D+i, C/ Espejo 2, Salamanca, 37007, Spain.
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57
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Agüero-Chapin G, Pérez-Machado G, Sánchez-Rodríguez A, Santos MM, Antunes A. Alignment-Free Methods for the Detection and Specificity Prediction of Adenylation Domains. Methods Mol Biol 2016; 1401:253-272. [PMID: 26831713 DOI: 10.1007/978-1-4939-3375-4_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Identifying adenylation domains (A-domains) and their substrate specificity can aid the detection of nonribosomal peptide synthetases (NRPS) at genome/proteome level and allow inferring the structure of oligopeptides with relevant biological activities. However, that is challenging task due to the high sequence diversity of A-domains (~10-40 % of amino acid identity) and their selectivity for 50 different natural/unnatural amino acids. Altogether these characteristics make their detection and the prediction of their substrate specificity a real challenge when using traditional sequence alignment methods, e.g., BLAST searches. In this chapter we describe two workflows based on alignment-free methods intended for the identification and substrate specificity prediction of A-domains. To identify A-domains we introduce a graphical-numerical method, implemented in TI2BioP version 2.0 (topological indices to biopolymers), which in a first step uses protein four-color maps to represent A-domains. In a second step, simple topological indices (TIs), called spectral moments, are derived from the graphical representations of known A-domains (positive dataset) and of unrelated but well-characterized sequences (negative set). Spectral moments are then used as input predictors for statistical classification techniques to build alignment-free models. Finally, the resulting alignment-free models can be used to explore entire proteomes for unannotated A-domains. In addition, this graphical-numerical methodology works as a sequence-search method that can be ensemble with homology-based tools to deeply explore the A-domain signature and cope with the diversity of this class (Aguero-Chapin et al., PLoS One 8(7):e65926, 2013). The second workflow for the prediction of A-domain's substrate specificity is based on alignment-free models constructed by transductive support vector machines (TSVMs) that incorporate information of uncharacterized A-domains. The construction of the models was implemented in the NRPSpredictor and in a first step uses the physicochemical fingerprint of the 34 residues lining the active site of the phenylalanine-adenylation domain of gramicidin synthetase A [PDB ID 1 amu] to derive a feature vector. Homologous positions were extracted for A-domains with known and unknown substrate specificities and turned into feature vectors. At the same time, A-domains with known specificities towards similar substrates were clustered by physicochemical properties of amino acids (AA). In a second step, support vector machines (SVMs) were optimized from feature vectors of characterized A-domains in each of the resulting clusters. Later, SVMs were used in the variant of TSVMs that integrate a fraction of uncharacterized A-domains during training to predict unknown specificities. Finally, uncharacterized A-domains were scored by each of the constructed alignment-free models (TSVM) representing each substrate specificity resulting from the clustering. The model producing the largest score for the uncharacterized A-domain assigns the substrate specificity to it (Rausch et al., Nucleic Acids Res 33:5799-5808, 2005).
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Affiliation(s)
- Guillermin Agüero-Chapin
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, Porto, 4050-123, Portugal
- Centro de Bioactivos Químicos, Universidad Central "Marta Abreu" de Las Villas (UCLV), Santa Clara, 54830, Cuba
| | - Gisselle Pérez-Machado
- Centro de Bioactivos Químicos, Universidad Central "Marta Abreu" de Las Villas (UCLV), Santa Clara, 54830, Cuba
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Naturales, Universidad Técnica Particular de Loja, San Cayetano Alto, S/N, Loja, Ecuador
| | - Miguel Machado Santos
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, Porto, 4050-123, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, 4169-007, Portugal
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, Porto, 4050-123, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, 4169-007, Portugal.
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58
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Harden BJ, Mishra SH, Frueh DP. Effortless assignment with 4D covariance sequential correlation maps. J Magn Reson 2015; 260:83-8. [PMID: 26432397 PMCID: PMC4628886 DOI: 10.1016/j.jmr.2015.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/11/2015] [Indexed: 05/13/2023]
Abstract
Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase.
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Affiliation(s)
- Bradley J Harden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 701 Hunterian, 725 N Wolfe St, Baltimore, MD 21205, United States
| | - Subrata H Mishra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 701 Hunterian, 725 N Wolfe St, Baltimore, MD 21205, United States
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 701 Hunterian, 725 N Wolfe St, Baltimore, MD 21205, United States
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59
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Barajas JF, Phelan RM, Schaub AJ, Kliewer JT, Kelly PJ, Jackson DR, Luo R, Keasling JD, Tsai SC. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols. ACTA ACUST UNITED AC 2015; 22:1018-29. [PMID: 26235055 DOI: 10.1016/j.chembiol.2015.06.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/05/2015] [Accepted: 06/22/2015] [Indexed: 01/22/2023]
Abstract
The terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite widespread use in nature, a lack of structural and mechanistic information concerning reductive release from polyketide synthase (PKS) and NRPS assembly lines principally limits our ability to redesign R domains with altered or improved activity. Here we report crystal structures for MxaA R, both in the absence and, for the first time, in the presence of the NADPH cofactor. Molecular dynamics simulations were employed to provide a deeper understanding of this domain and further identify residues critical for structural integrity, substrate binding, and catalysis. Aggregate computational and structural findings provided a basis for mechanistic investigations and, in the process, delivered a rationally altered variant with improved activity toward highly reduced substrates.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryan M Phelan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA
| | - Andrew J Schaub
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jaclyn T Kliewer
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Peter J Kelly
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - David R Jackson
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jay D Keasling
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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60
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Šink R, Barreteau H, Patin D, Mengin-Lecreulx D, Gobec S, Blanot D. MurD enzymes: some recent developments. Biomol Concepts 2015; 4:539-56. [PMID: 25436755 DOI: 10.1515/bmc-2013-0024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/10/2013] [Indexed: 12/21/2022] Open
Abstract
The synthesis of the peptide stem of bacterial peptidoglycan involves four enzymes, the Mur ligases (MurC, D, E and F). Among them, MurD is responsible for the ATP-dependent addition of d-glutamic acid to UDP-MurNAc-l-Ala, a reaction which involves acyl-phosphate and tetrahedral intermediates. Like most enzymes of peptidoglycan biosynthesis, MurD constitutes an attractive target for the design and synthesis of new antibacterial agents. Escherichia coli MurD has been the first Mur ligase for which the tridimensional (3D) structure was solved. Thereafter, several co-crystal structures with different ligands or inhibitors were released. In the present review, we will deal with work performed on substrate specificity, reaction mechanism and 3D structure of E. coli MurD. Then, a part of the review will be devoted to recent work on MurD orthologs from species other than E. coli and to cellular organization of Mur ligases and in vivo regulation of the MurD activity. Finally, we will review the different classes of MurD inhibitors that have been designed and assayed to date with the hope of obtaining new antibacterial compounds.
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61
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Garnham CP, Vemu A, Wilson-Kubalek EM, Yu I, Szyk A, Lander GC, Milligan RA, Roll-Mecak A. Multivalent Microtubule Recognition by Tubulin Tyrosine Ligase-like Family Glutamylases. Cell 2015; 161:1112-1123. [PMID: 25959773 DOI: 10.1016/j.cell.2015.04.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 01/29/2015] [Accepted: 03/11/2015] [Indexed: 12/30/2022]
Abstract
Glutamylation, the most prevalent tubulin posttranslational modification, marks stable microtubules and regulates recruitment and activity of microtubule- interacting proteins. Nine enzymes of the tubulin tyrosine ligase-like (TTLL) family catalyze glutamylation. TTLL7, the most abundant neuronal glutamylase, adds glutamates preferentially to the β-tubulin tail. Coupled with ensemble and single-molecule biochemistry, our hybrid X-ray and cryo-electron microscopy structure of TTLL7 bound to the microtubule delineates a tripartite microtubule recognition strategy. The enzyme uses its core to engage the disordered anionic tails of α- and β-tubulin, and a flexible cationic domain to bind the microtubule and position itself for β-tail modification. Furthermore, we demonstrate that all single-chain TTLLs with known glutamylase activity utilize a cationic microtubule-binding domain analogous to that of TTLL7. Therefore, our work reveals the combined use of folded and intrinsically disordered substrate recognition elements as the molecular basis for specificity among the enzymes primarily responsible for chemically diversifying cellular microtubules.
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Affiliation(s)
- Christopher P Garnham
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Annapurna Vemu
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | | | - Ian Yu
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Agnieszka Szyk
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | | | | | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA; National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA.
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62
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Hara R, Suzuki R, Kino K. Hydroxamate-based colorimetric assay to assess amide bond formation by adenylation domain of nonribosomal peptide synthetases. Anal Biochem 2015; 477:89-91. [PMID: 25615416 DOI: 10.1016/j.ab.2015.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/26/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022]
Abstract
We demonstrated the usefulness of a hydroxamate-based colorimetric assay for predicting amide bond formation (through an aminoacyl-AMP intermediate) by the adenylation domain of nonribosomal peptide synthetases. By using a typical adenylation domain of tyrocidine synthetase (involved in tyrocidine biosynthesis), we confirmed the correlation between the absorbance at 490 nm of the l-Trp-hydroxamate-Fe(3+) complex and the formation of l-Trp-l-Pro, where l-Pro was used instead of hydroxylamine. Furthermore, this assay was adapted to the adenylation domains of surfactin synthetase (involved in surfactin biosynthesis) and bacitracin synthetase (involved in bacitracin biosynthesis). Consequently, the formation of various aminoacyl l-Pro formations was observed.
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Affiliation(s)
- Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Ryohei Suzuki
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan; Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan.
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63
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Paulin S, Jamshad M, Dafforn TR, Garcia-Lara J, Foster SJ, Galley NF, Roper DI, Rosado H, Taylor PW. Surfactant-free purification of membrane protein complexes from bacteria: application to the staphylococcal penicillin-binding protein complex PBP2/PBP2a. Nanotechnology 2014; 25:285101. [PMID: 24972373 DOI: 10.1088/0957-4484/25/28/285101] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Surfactant-mediated removal of proteins from biomembranes invariably results in partial or complete loss of function and disassembly of multi-protein complexes. We determined the capacity of styrene-co-maleic acid (SMA) co-polymer to remove components of the cell division machinery from the membrane of drug-resistant staphylococcal cells. SMA-lipid nanoparticles solubilized FtsZ-PBP2-PBP2a complexes from intact cells, demonstrating the close physical proximity of these proteins within the lipid bilayer. Exposure of bacteria to (-)-epicatechin gallate, a polyphenolic agent that abolishes β-lactam resistance in staphylococci, disrupted the association between PBP2 and PBP2a. Thus, SMA purification provides a means to remove native integral membrane protein assemblages with minimal physical disruption and shows promise as a tool for the interrogation of molecular aspects of bacterial membrane protein structure and function.
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Affiliation(s)
- Sarah Paulin
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
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Gao X, Jiang W, Jiménez-Osés G, Choi MS, Houk KN, Tang Y, Walsh CT. An iterative, bimodular nonribosomal peptide synthetase that converts anthranilate and tryptophan into tetracyclic asperlicins. ACTA ACUST UNITED AC 2014; 20:870-8. [PMID: 23890005 DOI: 10.1016/j.chembiol.2013.04.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/24/2013] [Accepted: 04/30/2013] [Indexed: 02/02/2023]
Abstract
The bimodular 276 kDa nonribosomal peptide synthetase AspA from Aspergillus alliaceus, heterologously expressed in Saccharomyces cerevisiae, converts tryptophan and two molecules of the aromatic β-amino acid anthranilate (Ant) into a pair of tetracyclic peptidyl alkaloids asperlicin C and D in a ratio of 10:1. The first module of AspA activates and processes two molecules of Ant iteratively to generate a tethered Ant-Ant-Trp-S-enzyme intermediate on module two. Release is postulated to involve tandem cyclizations, in which the first step is the macrocyclization of the linear tripeptidyl-S-enzyme, by the terminal condensation (CT) domain to generate the regioisomeric tetracyclic asperlicin scaffolds. Computational analysis of the transannular cyclization of the 11-membered macrocyclic intermediate shows that asperlicin C is the kinetically favored product due to the high stability of a conformation resembling the transition state for cyclization, while asperlicin D is thermodynamically more stable.
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Affiliation(s)
- Xue Gao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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Moutiez M, Seguin J, Fonvielle M, Belin P, Jacques IB, Favry E, Arthur M, Gondry M. Specificity determinants for the two tRNA substrates of the cyclodipeptide synthase AlbC from Streptomyces noursei. Nucleic Acids Res 2014; 42:7247-58. [PMID: 24782519 PMCID: PMC4066775 DOI: 10.1093/nar/gku348] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNA substrates in a sequential ping-pong mechanism to form a cyclodipeptide. The crystal structures of three CDPSs have been determined and all show a Rossmann-fold domain similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs). Structural features and mutational analyses however suggest that CDPSs and aaRSs interact differently with their tRNA substrates. We used AlbC from Streptomyces noursei that mainly produces cyclo(l-Phe-l-Leu) to investigate the interaction of a CDPS with its substrates. We demonstrate that Phe-tRNAPhe is the first substrate accommodated by AlbC. Its binding to AlbC is dependent on basic residues located in the helix α4 that form a basic patch at the surface of the protein. AlbC does not use all of the Leu-tRNALeu isoacceptors as a second substrate. We show that the G1-C72 pair of the acceptor stem is essential for the recognition of the second substrate. Substitution of D163 located in the loop α6–α7 or D205 located in the loop β6–α8 affected Leu-tRNALeu isoacceptors specificity, suggesting the involvement of these residues in the binding of the second substrate. This is the first demonstration that the two substrates of CDPSs are accommodated in different binding sites.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- Binding Sites
- Peptide Synthases/chemistry
- Peptide Synthases/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Streptomyces/enzymology
- Substrate Specificity
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Affiliation(s)
- Mireille Moutiez
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Jérôme Seguin
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Matthieu Fonvielle
- INSERM, U1138, LRMA, Equipe 12 du Centre de Recherche des Cordeliers, Paris 75006, France Université Pierre et Marie Curie, UMR S 1138, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR S 1138, Paris, France
| | - Pascal Belin
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Isabelle Béatrice Jacques
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Emmanuel Favry
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
| | - Michel Arthur
- INSERM, U1138, LRMA, Equipe 12 du Centre de Recherche des Cordeliers, Paris 75006, France Université Pierre et Marie Curie, UMR S 1138, Paris, France Université Paris Descartes, Sorbonne Paris Cité, UMR S 1138, Paris, France
| | - Muriel Gondry
- Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette Cedex, France
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66
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Fukuda T, Sudoh Y, Tsuchiya Y, Okuda T, Igarashi Y. Isolation and biosynthesis of preussin B, a pyrrolidine alkaloid from Simplicillium lanosoniveum. J Nat Prod 2014; 77:813-817. [PMID: 24588303 DOI: 10.1021/np400910r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A new pyrrolidine alkaloid, preussin B (1), was isolated from the culture extract of the fungus Simplicillium lanosoniveum TAMA 173 along with the known congener preussin (2). The structure and absolute configuration of 1 were determined by spectroscopic analysis and spectral comparison with 2. Feeding experiments with 13C-labeled precursors revealed that the pyrrolidine ring of 1 was assembled from acetate and l-phenylalanine by a PKS-NRPS hybrid biosynthetic pathway.
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Affiliation(s)
- Takao Fukuda
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University , 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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67
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Huynh KH, Tran HT, Pham TV, Ngo HPT, Cha SS, Chung KM, Lee SH, Kang LW. Expression, crystallization and preliminary X-ray crystallographic analysis of D-alanine-D-alanine ligase from OXA-23-producing Acinetobacter baumannii K0420859. Acta Crystallogr F Struct Biol Commun 2014; 70:505-8. [PMID: 24699750 PMCID: PMC3976074 DOI: 10.1107/s2053230x14005081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/05/2014] [Indexed: 11/10/2022] Open
Abstract
Acinetobacter baumannii causes bacteraemia, pneumonia, other respiratory-tract and urinary-tract infections in humans. OXA-23 carbapenemase-producing A. baumannii K0420859 (A. baumannii OXA-23) is resistant to carbapenem, a common antibacterial drug. To develop an efficient and novel antibacterial drug against A. baumannii OXA-23, D-alanine-D-alanine ligase, which is essential in bacterial cell-wall synthesis, is of interest. Here, the D-alanine-D-alanine ligase (AbDdl) gene from A. baumannii OXA-23 was cloned and expressed, and the AbDdl protein was purified and crystallized; this enzyme can be used as a novel target for an antibacterial drug against A. baumannii OXA-23. The AbDdl crystal diffracted to a resolution of 2.8 Å and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 113.4, b = 116.7, c = 176.5 Å, a corresponding VM of 2.8 Å(3) Da(-1) and a solvent content of 56.3%, and six protomers in the asymmetric unit.
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Affiliation(s)
- Kim-Hung Huynh
- Department of Biological Sciences, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Huyen-Thi Tran
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Tan-Viet Pham
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea
| | - Kyung Min Chung
- Department of Microbiology and Immunology, Chonbuk National University Medical School, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 449-728, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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68
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Wang M, Beissner M, Zhao H. Aryl-aldehyde formation in fungal polyketides: discovery and characterization of a distinct biosynthetic mechanism. Chem Biol 2014; 21:257-63. [PMID: 24412543 PMCID: PMC3943900 DOI: 10.1016/j.chembiol.2013.12.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 12/02/2013] [Accepted: 12/07/2013] [Indexed: 11/22/2022]
Abstract
Aryl-aldehydes are a common feature in fungal polyketides, which are considered to be exclusively generated by the R domain of nonreducing polyketide synthases (NR-PKSs). However, by cloning and heterologous expression of both cryptic NR-PKS and nonribosomal peptide synthase (NRPS)-like genes from Aspergillus terreus in Saccharomyces cerevisiae, we identified a distinct mechanism for aryl-aldehyde formation in which a NRPS-like protein activates and reduces an aryl-acid produced by the accompanying NR-PKS to an aryl-aldehyde. Bioinformatics study indicates that such a mechanism may be widely used throughout the fungi kingdom.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mirko Beissner
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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69
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Bosello M, Zeyadi M, Kraas FI, Linne U, Xie X, Marahiel MA. Structural characterization of the heterobactin siderophores from Rhodococcus erythropolis PR4 and elucidation of their biosynthetic machinery. J Nat Prod 2013; 76:2282-2290. [PMID: 24274668 DOI: 10.1021/np4006579] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this study, the isolation, the structural characterization, and the elucidation of the biosynthetic origin of heterobactins, catecholate-hydroxamate mixed-type siderophores from Rhodococcus erythropolis PR4, are reported. The structure elucidation of heterobactin A was accomplished via MS(n) analysis and NMR spectroscopy and revealed the noteworthy presence of a peptide bond between the guanidine group of an arginine residue and a 2,3-dihydroxybenzoate moiety. The two heterobactin S1 and S2 variants are derivatives of heterobactin A that have sulfonation modifications on the aromatic rings. The bioinformatic analysis of the R. erythropolis PR4 genome and the subsequent genetic and biochemical characterization of the putative biosynthetic machinery identified the gene cluster responsible for the biosynthesis of the heterobactins. Interestingly, the HtbG NRPS presents an unprecedented C-PCP-A domain organization within the second module of the synthetase that may help the correct elongation of the peptide intermediate. Finally, the present work revises the structure of heterobactin A that was described by Carrano et al. in 2001.
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Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg , Hans-Meerwein-Strasse D-35043 Marburg, Germany
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70
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Li H, Tanikawa T, Sato Y, Nakagawa Y, Matsuyama T. Serratia marcescensGene Required for Surfactant Serrawettin W1 Production Encodes Putative Aminolipid Synthetase Belonging to Nonribosomal Peptide Synthetase Family. Microbiol Immunol 2013; 49:303-10. [PMID: 15840955 DOI: 10.1111/j.1348-0421.2005.tb03734.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Serrawettin W1 produced by Serratia marcescens is a surface active exolipid having various functions supporting behaviors of bacteria on surface environments. Through the genetic analyses of serrawettin-less mutants of S. marcescens 274, the swrW gene encoding putative serrawettin W1 synthetase was identified. Homology analysis of the putative SwrW demonstrated the presence of condensation, adenylation, thiolation, and thioesterase domains which are characteristic for nonribosomal peptide synthetase (NRPS). NRPSs have been known as multi-modular enzymes. Linear alignment of these modules specifying respective amino acids will enable peptide bond formation resulting in a specific amino acid sequence. Putative SwrW was uni-modular NRPS specifying only L-serine. Possible steps in this simple unimodular NRPS for biosynthesis of serrawettin W1 [ cyclo-(D-3-hydroxydecanoyl-L-seryl) (2) ] were predicted by referring to the ingenious enzymatic activity of gramicidin S synthetase (multi-modular NRPS) of Brevibacillus brevis.
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Affiliation(s)
- Hong Li
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
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71
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Mizuno CM, Kimes NE, López-Pérez M, Ausó E, Rodriguez-Valera F, Ghai R. A hybrid NRPS-PKS gene cluster related to the bleomycin family of antitumor antibiotics in Alteromonas macleodii strains. PLoS One 2013; 8:e76021. [PMID: 24069455 PMCID: PMC3777966 DOI: 10.1371/journal.pone.0076021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/19/2013] [Indexed: 11/24/2022] Open
Abstract
Although numerous marine bacteria are known to produce antibiotics via hybrid NRPS-PKS gene clusters, none have been previously described in an Alteromonas species. In this study, we describe in detail a novel hybrid NRPS-PKS cluster identified in the plasmid of the Alteromonasmacleodii strain AltDE1 and analyze its relatedness to other similar gene clusters in a sequence-based characterization. This is a mobile cluster, flanked by transposase-like genes, that has even been found inserted into the chromosome of some Alteromonasmacleodii strains. The cluster contains separate genes for NRPS and PKS activity. The sole PKS gene appears to carry a novel acyltransferase domain, quite divergent from those currently characterized. The predicted specificities of the adenylation domains of the NRPS genes suggest that the final compound has a backbone very similar to bleomycin related compounds. However, the lack of genes involved in sugar biosynthesis indicates that the final product is not a glycopeptide. Even in the absence of these genes, the presence of the cluster appears to confer complete or partial resistance to phleomycin, which may be attributed to a bleomycin-resistance-like protein identified within the cluster. This also suggests that the compound still shares significant structural similarity to bleomycin. Moreover, transcriptomic evidence indicates that the NRPS-PKS cluster is expressed. Such sequence-based approaches will be crucial to fully explore and analyze the diversity and potential of secondary metabolite production, especially from increasingly important sources like marine microbes.
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Affiliation(s)
- Carolina Megumi Mizuno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Nikole E. Kimes
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Eva Ausó
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- * E-mail:
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiologia, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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72
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Kim MK, An YJ, Cha SS. The crystal structure of a novel phosphopantothenate synthetase from the hyperthermophilic archaea, Thermococcus onnurineus NA1. Biochem Biophys Res Commun 2013; 439:533-8. [PMID: 24021277 DOI: 10.1016/j.bbrc.2013.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 11/18/2022]
Abstract
Pantothenate is the essential precursor of coenzyme A (CoA), a fundamental cofactor in all aspects of metabolism. In bacteria and eukaryotes, pantothenate synthetase (PS) catalyzes the last step in the pantothenate biosynthetic pathway, and pantothenate kinase (PanK) phosphorylates pantothenate for its entry into the CoA biosynthetic pathway. However, genes encoding PS and PanK have not been identified in archaeal genomes. Recently, a comparative genomic analysis and the identification and characterization of two novel archaea-specific enzymes show that archaeal pantoate kinase (PoK) and phosphopantothenate synthetase (PPS) represent counterparts to the PS/PanK pathway in bacteria and eukaryotes. The TON1374 protein from Thermococcus onnurineus NA1 is a PPS, that shares 54% sequence identity with the first reported archaeal PPS candidate, MM2281, from Methanosarcina mazei and 91% sequence identity with TK1686, the PPS from Thermococcus kodakarensis. Here, we report the apo and ATP-complex structures of TON1374 and discuss the substrate-binding mode and reaction mechanism.
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Affiliation(s)
- Min-Kyu Kim
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea
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73
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Sundlov JA, Gulick AM. Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry. Acta Crystallogr D Biol Crystallogr 2013; 69:1482-92. [PMID: 23897471 PMCID: PMC3727328 DOI: 10.1107/s0907444913009372] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/07/2013] [Indexed: 12/21/2022]
Abstract
The nonribosomal peptide synthetases (NRPSs) are a family of modular proteins that contain multiple catalytic domains joined in a single protein. Together, these domains work to produce chemically diverse peptides, including compounds with antibiotic activity or that play a role in iron acquisition. Understanding the structural mechanisms that govern the domain interactions has been a long-standing goal. During NRPS synthesis, amino-acid substrates are loaded onto integrated carrier protein domains through the activity of NRPS adenylation domains. The structures of two adenylation domain-carrier protein domain complexes have recently been determined in an effort that required the use of a mechanism-based inhibitor to trap the domain interaction. Here, the continued analysis of these proteins is presented, including a higher resolution structure of an engineered di-domain protein containing the EntE adenylation domain fused with the carrier protein domain of its partner EntB. The protein crystallized in a novel space group in which molecular replacement and refinement were challenged by noncrystallographic pseudo-translational symmetry. The structure determination and how the molecular packing impacted the diffraction intensities are reported. Importantly, the structure illustrates that in this new crystal form the functional interface between the adenylation domain and the carrier protein domain remains the same as that observed previously. At a resolution that allows inclusion of water molecules, additional interactions are observed between the two protein domains and between the protein and its ligands. In particular, a highly solvated region that surrounds the carrier protein cofactor is described.
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Affiliation(s)
- Jesse A. Sundlov
- Hauptman–Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Andrew M. Gulick
- Hauptman–Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
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74
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Gaudelli NM, Townsend CA. Stereocontrolled syntheses of peptide thioesters containing modified seryl residues as probes of antibiotic biosynthesis. J Org Chem 2013; 78:6412-26. [PMID: 23758494 PMCID: PMC3898789 DOI: 10.1021/jo4007893] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methods have been developed to synthesize tri- and pentapeptide thioesters containing one or more p-(hydroxyphenyl)glycine (pHPG) residues and L-serine, some where the latter is O-phosphorylated, O-acetylated, or exists as a β-lactam. Selection of orthogonal protection strategies and development of conditions to achieve seryl O-phosphorylation without β-elimination and to maintain stereochemical control, especially simultaneously at exceptionally base-labile pHPG α-carbons, are described. Intramolecular closure of a seryl peptide to a β-lactam-containing peptide and the syntheses of corresponding thioester analogues are also reported. Modification of classical Mitsunobu conditions is described in the synthesis of the β-lactam-containing products, and in a broadly useful observation, it was found that simple exclusion of light from the P(OEt)3-mediated Mitsunobu ring closure afforded yields of >95%, presumably owing to reduced photodegradation of the azodicarboxylate used. These sensitive potential substrates and products will be used in mechanistic studies of the two nonribosomal peptide synthetases NocA and NocB that lie at the heart of nocardicin biosynthesis, a family of monocyclic β-lactam antibiotics.
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Affiliation(s)
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
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75
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Sangiambut S, Channon K, Thomson NM, Sato S, Tsuge T, Doi Y, Sivaniah E. A robust route to enzymatically functional, hierarchically self-assembled peptide frameworks. Adv Mater 2013; 25:2661-2665. [PMID: 23341342 DOI: 10.1002/adma.201204127] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/21/2012] [Indexed: 06/01/2023]
Abstract
The addition of enzyme biofunctionality to self-assembling peptide nanofibers is challenging since such additions can inhibit functionality or self-assembly. We introduce a method for peptide nanofiber enzyme functionalization, demonstrated by the attachment of a polymerization synthase to peptide nanofibers. The enzyme generates a biocompatible, biodegradable biopolyester coat on the fibers with applicablity in medical engineering. This approach provides a template for generation of functional bionanomaterials.
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Affiliation(s)
- S Sangiambut
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, CB3 0HE, UK
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76
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Liu L, Lu Z, Lv F, Zhang C, Bie X. [Activity of the SrfAC-A domain from Bacillus subtilis fmbj]. Wei Sheng Wu Xue Bao 2013; 53:437-443. [PMID: 23957147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVE We studied the A domain of surfactin synthase in vitro to obtain new surfactin analogues. METHODS We cloned the srfAC-A gene from Bacillus subtilis fmbj by PCR, and constructed a recombinant expression vector named pET-23a-srfAC-A. Furthermore, the SrfAC-A domain was expressed in E. coli BL21 (DE3) and purified by Ni-NTA agarose column. Then the activity of srfAC-A domain was detected. RESULTS The srfAC-A domain had specificity towards Ile, but almost no activity to other amino acids. CONCLUSION The independent A domain from surfactin synthase had selectivity to specific amino acids in vitro.
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Affiliation(s)
- Lixia Liu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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77
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Nogaret S, Guittet E, Birlirakis N. (1)H, (13)C and (15)N NMR assignment of CGC-19, a single domain proteic constituent of a non ribosomal peptide synthetase. Biomol NMR Assign 2013; 7:1-4. [PMID: 22419055 DOI: 10.1007/s12104-012-9364-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 02/20/2012] [Indexed: 05/31/2023]
Abstract
CGC-19, a 14 kDa proteic constituent of a non ribosomal peptide synthetase implicated in the biosynthesis of a secondary metabolite in Streptomyces ambofaciens, has been isotopically enriched and recombinantly expressed. Its nearly complete (1)H, (13)C and (15)N resonance assignment is reported hereunder.
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Affiliation(s)
- Sophie Nogaret
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Bât. 23B, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
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Wilson DJ, Shi C, Teitelbaum AM, Gulick AM, Aldrich CC. Characterization of AusA: a dimodular nonribosomal peptide synthetase responsible for the production of aureusimine pyrazinones. Biochemistry 2013; 52:926-37. [PMID: 23302043 PMCID: PMC3577359 DOI: 10.1021/bi301330q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aureusimines have been identified as potential virulence factors in Staphylococcus aureus. These pyrazinone secondary metabolites are produced by a nonribosomal peptide synthetase (NRPS) annotated as AusA. We report the overproduction of AusA as a 277 kDa soluble protein with A(1)-T(1)-C-A(2)-T(2)-R bimodular architecture. The substrate specificity of each adenylation (A) domain was initially probed using an ATP-pyrophosphate exchange assay with A-domain selective bisubstrate inhibitors to chemically knock out each companion A-domain. The activity of AusA was then reconstituted in vitro and shown to produce all naturally occurring aureusimines and non-natural pyrazinone products with k(cat) values ranging from 0.4 to 1.3 min(-1). Steady-state kinetic parameters were determined for all substrates and cofactors, providing the first comprehensive steady-state characterization of a NRPS employing a product formation assay. The K(M) values for the amino acids were up to 60-fold lower with the product formation assay than with the ATP-pyrophosphate exchange assay, most commonly used to assess A-domain substrate specificity. The C-terminal reductase (R) domain catalyzes reductive release of the dipeptidyl intermediate, leading to formation of an amino aldehyde that cyclizes to a dihydropyrazinone. We show oxidation to the final pyrazinone heterocycle is spontaneous. The activity and specificity of the R-domain was independently investigated using a NADPH consumption assay. AusA is a minimal autonomous two-module NRPS that represents an excellent model system for further kinetic and structural characterization.
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Affiliation(s)
- Daniel J. Wilson
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ce Shi
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
| | - Aaron M. Teitelbaum
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, MN 55455
| | - Andrew M. Gulick
- Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY, 14203 USA
| | - Courtney C. Aldrich
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455
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79
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Simčič M, Sosič I, Hodošček M, Barreteau H, Blanot D, Gobec S, Grdadolnik SG. The binding mode of second-generation sulfonamide inhibitors of MurD: clues for rational design of potent MurD inhibitors. PLoS One 2012; 7:e52817. [PMID: 23285193 PMCID: PMC3527612 DOI: 10.1371/journal.pone.0052817] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/23/2012] [Indexed: 11/19/2022] Open
Abstract
A series of optimized sulfonamide derivatives was recently reported as novel inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). These are based on naphthalene-N-sulfonyl-D-glutamic acid and have the D-glutamic acid replaced with rigidified mimetics. Here we have defined the binding site of these novel ligands to MurD using (1)H/(13)C heteronuclear single quantum correlation. The MurD protein was selectively (13)C-labeled on the methyl groups of Ile (δ1 only), Leu and Val, and was isolated and purified. Crucial Ile, Leu and Val methyl groups in the vicinity of the ligand binding site were identified by comparison of chemical shift perturbation patterns among the ligands with various structural elements and known binding modes. The conformational and dynamic properties of the bound ligands and their binding interactions were examined using the transferred nuclear Overhauser effect and saturation transfer difference. In addition, the binding mode of these novel inhibitors was thoroughly examined using unrestrained molecular dynamics simulations. Our results reveal the complex dynamic behavior of ligand-MurD complexes and its influence on ligand-enzyme contacts. We further present important findings for the rational design of potent Mur ligase inhibitors.
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Affiliation(s)
- Mihael Simčič
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Milan Hodošček
- Laboratory of Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, Orsay, France
| | - Didier Blanot
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, Orsay, France
- Centre National de la Recherche Scientifique, Orsay, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Simona Golič Grdadolnik
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Ljubljana, Slovenia
- * E-mail:
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80
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Brants J, Semenchenko K, Wasylyk C, Robert A, Carles A, Zambrano A, Pradeau-Aubreton K, Birck C, Schalken JA, Poch O, de Mey J, Wasylyk B. Tubulin tyrosine ligase like 12, a TTLL family member with SET- and TTL-like domains and roles in histone and tubulin modifications and mitosis. PLoS One 2012; 7:e51258. [PMID: 23251473 PMCID: PMC3520985 DOI: 10.1371/journal.pone.0051258] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/30/2012] [Indexed: 01/15/2023] Open
Abstract
hTTLL12 is a member of the tubulin tyrosine ligase (TTL) family that is highly conserved in phylogeny. It has both SET-like and TTL-like domains, suggesting that it could have histone methylation and tubulin tyrosine ligase activities. Altered expression of hTTLL12 in human cells leads to specific changes in H4K20 trimethylation, and tubulin detyrosination, hTTLL12 does not catalyse histone methylation or tubulin tyrosination in vitro, as might be expected from the lack of critical amino acids in its SET-like and TTLL-like domains. hTTLL12 misexpression increases mitotic duration and chromosome numbers. These results suggest that hTTLL12 has non-catalytic functions related to tubulin and histone modification, which could be linked to its effects on mitosis and chromosome number stability.
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Affiliation(s)
- Jan Brants
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Kostyantyn Semenchenko
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Christine Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Aude Robert
- Université de Strasbourg, Ecole Supérieure de Biotechnologie de Strasbourg C.N.R.S. - U.M.R.7100, Equipe “Microtubules et Morphogenèse”, Parc d'Innovation, Illkirch, France
| | - Annaick Carles
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Alberto Zambrano
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Karine Pradeau-Aubreton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Jack A. Schalken
- Department of Urology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Olivier Poch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
| | - Jan de Mey
- Université de Strasbourg, Ecole Supérieure de Biotechnologie de Strasbourg C.N.R.S. - U.M.R.7100, Equipe “Microtubules et Morphogenèse”, Parc d'Innovation, Illkirch, France
| | - Bohdan Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104 CNRS UDS - U 964 INSERM , Illkirch, France
- * E-mail:
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81
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Chen W, Zhu P, He S, Jin H, Yan X. [Nonribosomal peptides synthetases gene clusters and core domain in Pseudoalteromonas sp. NJ631]. Wei Sheng Wu Xue Bao 2012; 52:1531-1539. [PMID: 23457803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
OBJECTIVE We studied nonribosomal peptides synthetases (NRPSs) gene clusters and the core module of NRPSs in Pseudoalteromonas sp. NJ631 using genome mining approach. METHODS The genome of Pseudoalteromonas sp. NJ631 was constructed by the next genome sequencing (NGS) technology. We adopted an online available software called NRPS-PKS knowledgebase to identify potential NRPSs gene clusters within genes involved in the biosynthesis of secondary metabolite of Pseudoalteromonas sp. NJ631. The genes encoding adenylation (A) domains, the core module of NRPSs, were collected and analyzed using genome mining method. RESULTS We identified three typical NRPS gene clusters comprising three ORFs which encode six continuous modular NRPSs. The result of genome mining indicates that genome of Pseudoalteromonas sp. NJ631 contains 38 A domain genes which show 60% similarity below to their closest relatives. The substrate of these A domains was predicted to specifically bind 18 types of amino acids using the specificity-conferring selection rule. CONCLUSION This is the first reported on the systematic screening and analysis of NRPSs gene clusters and A domains in genus Pseudoalteromonas, suggesting that the genus Pseudoalteromonas possesses a vast array of secondary metabolite biosynthesis genes that were previously found mostly in actinomycetes and fungi. The information on secondary metabolite genes from Pseudoalteromonas sp. NJ631 will facilitate us to isolate novel nonribosomal peptides.
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Affiliation(s)
- Wei Chen
- Key Laboratory of Applied Marine Biotechnology, (Ningbo University), Ministry of Education, Ningbo, Zhejiang 315211, China.
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82
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Abstract
Structural biology has provided significant insights into the complex chemistry and macromolecular organization of nonribosomal peptide synthetases. In addition, novel pathways are continually described, expanding the knowledge of known biosynthetic chemistry.
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Affiliation(s)
- Heather L. Condurso
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
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83
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Škedelj V, Arsovska E, Tomašić T, Kroflič A, Hodnik V, Hrast M, Bešter-Rogač M, Anderluh G, Gobec S, Bostock J, Chopra I, O'Neill AJ, Randall C, Zega A. 6-Arylpyrido[2,3-d]pyrimidines as novel ATP-competitive inhibitors of bacterial D-alanine:D-alanine ligase. PLoS One 2012; 7:e39922. [PMID: 22876277 PMCID: PMC3410885 DOI: 10.1371/journal.pone.0039922] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 05/29/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND ATP-dependent D-alanine:D-alanine ligase (Ddl) is a part of biochemical machinery involved in peptidoglycan biosynthesis, as it catalyzes the formation of the terminal D-ala-D-ala dipeptide of the peptidoglycan precursor UDPMurNAc-pentapeptide. Inhibition of Ddl prevents bacterial growth, which makes this enzyme an attractive and viable target in the urgent search of novel effective antimicrobial drugs. To address the problem of a relentless increase in resistance to known antimicrobial agents we focused our attention to discovery of novel ATP-competitive inhibitors of Ddl. METHODOLOGY/PRINCIPAL FINDINGS Encouraged by recent successful attempts to find selective ATP-competitive inhibitors of bacterial enzymes we designed, synthesized and evaluated a library of 6-arylpyrido[2,3-d]pyrimidine-based compounds as inhibitors of Escherichia coli DdlB. Inhibitor binding to the target enzyme was subsequently confirmed by surface plasmon resonance and studied with isothermal titration calorimetry. Since kinetic analysis indicated that 6-arylpyrido[2,3-d]pyrimidines compete with the enzyme substrate ATP, inhibitor binding to the ATP-binding site was additionally studied with docking. Some of these inhibitors were found to possess antibacterial activity against membrane-compromised and efflux pump-deficient strains of E. coli. CONCLUSIONS/SIGNIFICANCE We discovered new ATP-competitive inhibitors of DdlB, which may serve as a starting point for development of more potent inhibitors of DdlB that could include both, an ATP-competitive and D-Ala competitive moiety.
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Affiliation(s)
- Veronika Škedelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Emilija Arsovska
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Tihomir Tomašić
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Kroflič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Vesna Hodnik
- Biotechnical faculty, Infrastructural Center for Surface Plasmon Resonance, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Marija Bešter-Rogač
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Anderluh
- Biotechnical faculty, Infrastructural Center for Surface Plasmon Resonance, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Julieanne Bostock
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ian Chopra
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alex J. O'Neill
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Christopher Randall
- Antimicrobial Research Centre and Instititue of Molecular & Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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84
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Abstract
Many pharmaceuticals on the market today belong to a large class of natural products called nonribosomal peptides (NRPs). Originating from bacteria and fungi, these peptide-based natural products consist not only of the 20 canonical L-amino acids, but also non-proteinogenic amino acids, heterocyclic rings, sugars, and fatty acids, generating tremendous chemical diversity. As a result, these secondary metabolites exhibit a broad array of bioactivity, ranging from antimicrobial to anticancer. The biosynthesis of these complex compounds is carried out by large multimodular megaenzymes called nonribosomal peptide synthetases (NRPSs). Each module is responsible for incorporation of a monomeric unit into the natural product peptide and is composed of individual domains that perform different catalytic reactions. Biochemical and bioinformatic investigations of these enzymes have uncovered the key principles of NRP synthesis, expanding the pharmaceutical potential of their enzymatic processes. Progress has been made in the manipulation of this biosynthetic machinery to develop new chemoenzymatic approaches for synthesizing novel pharmaceutical agents with increased potency. This review focuses on the recent discoveries and breakthroughs in the structural elucidation, molecular mechanism, and chemical biology underlying the discrete domains within NRPSs.
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85
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Nikolouli K, Mossialos D. Bioactive compounds synthesized by non-ribosomal peptide synthetases and type-I polyketide synthases discovered through genome-mining and metagenomics. Biotechnol Lett 2012; 34:1393-403. [PMID: 22481301 DOI: 10.1007/s10529-012-0919-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 03/21/2012] [Indexed: 12/16/2022]
Abstract
Non-ribosomal peptide synthetases (NRPS) and type-I polyketide synthases (PKS-I) are multimodular enzymes involved in biosynthesis of oligopeptide and polyketide secondary metabolites produced by microorganisms such as bacteria and fungi. New findings regarding the mechanisms underlying NRPS and PKS-I evolution illustrate how microorganisms expand their metabolic potential. During the last decade rapid development of bioinformatics tools as well as improved sequencing and annotation of microbial genomes led to discovery of novel bioactive compounds synthesized by NRPS and PKS-I through genome-mining. Taking advantage of these technological developments metagenomics is a fast growing research field which directly studies microbial genomes or specific gene groups and their products. Discovery of novel bioactive compounds synthesized by NRPS and PKS-I will certainly be accelerated through metagenomics, allowing the exploitation of so far untapped microbial resources in biotechnology and medicine.
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Affiliation(s)
- Katerina Nikolouli
- Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26 & Eolou, 41221, Larissa, Greece
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86
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Seguin J, Moutiez M, Li Y, Belin P, Lecoq A, Fonvielle M, Charbonnier JB, Pernodet JL, Gondry M. Nonribosomal peptide synthesis in animals: the cyclodipeptide synthase of Nematostella. ACTA ACUST UNITED AC 2012; 18:1362-8. [PMID: 22118670 DOI: 10.1016/j.chembiol.2011.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 09/02/2011] [Accepted: 09/23/2011] [Indexed: 01/10/2023]
Abstract
Cyclodipeptide synthases (CDPSs) are small enzymes structurally related to class-I aminoacyl-tRNA synthetases (aaRSs). They divert aminoacylated tRNAs from their canonical role in ribosomal protein synthesis, for cyclodipeptide formation. All the CDPSs experimentally characterized to date are bacterial. We show here that a predicted CDPS from the sea anemone Nematostella vectensis is an active CDPS catalyzing the formation of various cyclodipeptides, preferentially containing tryptophan. Our findings demonstrate that eukaryotes encode active CDPSs and suggest that all CDPSs have a similar aminoacyl-tRNA synthetase-like architecture and ping-pong mechanism. They also raise questions about the biological roles of the cyclodipeptides produced in bacteria and eukaryotes.
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Affiliation(s)
- Jérôme Seguin
- CEA, Institut de Biologie et Technologies de Saclay, F-91191 Gif-sur-Yvette, France
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87
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Tsuda T, Suzuki T, Kojima S. Crystallization and preliminary X-ray diffraction analysis of Bacillus subtilis YwfE, an L-amino-acid ligase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:203-6. [PMID: 22298000 PMCID: PMC3274404 DOI: 10.1107/s174430911105425x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 12/16/2011] [Indexed: 11/10/2022]
Abstract
Bacillus subtilis YwfE, an L-amino-acid ligase, catalyzes the formation of an α-dipeptide from L-amino acids in an ATP-dependent manner. In order to elucidate the substrate-recognition mode and the reaction mechanism of this ligase, native and selenomethionine-derivatized (SeMet) crystals of YwfE in the presence of ADP, MgCl(2) and the dipeptide L-Ala-L-Gln were obtained using the hanging-drop vapour-diffusion method. These crystals diffracted to 1.9 and 2.8 Å resolution, respectively. Preliminary SAD phase calculations using the data set from the SeMet crystal suggested that the crystal belonged to the hexagonal space group P6(5)22, with unit-cell parameters a = b = 90.85, c = 250.31 Å, and contained one molecule in the asymmetric unit with a solvent content of 57.3%.
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Affiliation(s)
- Takeo Tsuda
- Department of Life Science, Faculty of Science, Gakushuin University, Tokyo, Japan.
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88
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Orlova TI, Bulgakova VG, Polin AN. [Biologically active nonribosomal peptides. III. Mechanism of biosynthesis of nonribosomal peptides]. Antibiot Khimioter 2012; 57:43-54. [PMID: 23350194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The third part of the review is concerned with investigation of nonribosomal peptides.
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89
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Rehan AM, Bashiri G, Paterson NG, Baker EN, Squire CJ. Cloning, expression, purification, crystallization and preliminary X-ray studies of the C-terminal domain of Rv3262 (FbiB) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1274-7. [PMID: 22102046 PMCID: PMC3212381 DOI: 10.1107/s1744309111028958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 07/18/2011] [Indexed: 11/11/2022]
Abstract
During cofactor F(420) biosynthesis, the enzyme F(420)-γ-glutamyl ligase (FbiB) catalyzes the addition of γ-linked L-glutamate residues to form polyglutamylated F(420) derivatives. In Mycobacterium tuberculosis, Rv3262 (FbiB) consists of two domains: an N-terminal domain from the F(420) ligase superfamily and a C-terminal domain with sequence similarity to nitro-FMN reductase superfamily proteins. To characterize the role of the C-terminal domain of FbiB in polyglutamyl ligation, it has been purified and crystallized in an apo form. The crystals diffracted to 2.0 Å resolution using a synchrotron source and belonged to the tetragonal space group P4(1)2(1)2 (or P4(3)2(1)2), with unit-cell parameters a = b = 136.6, c = 101.7 Å, α = β = γ = 90°.
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Affiliation(s)
- Aisyah M Rehan
- Structural Biology Laboratory, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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90
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Zidar N, Tomašić T, Šink R, Kovač A, Patin D, Blanot D, Contreras-Martel C, Dessen A, Premru MM, Zega A, Gobec S, Mašič LP, Kikelj D. New 5-benzylidenethiazolidin-4-one inhibitors of bacterial MurD ligase: design, synthesis, crystal structures, and biological evaluation. Eur J Med Chem 2011; 46:5512-23. [PMID: 21963114 DOI: 10.1016/j.ejmech.2011.09.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 09/02/2011] [Accepted: 09/08/2011] [Indexed: 11/19/2022]
Abstract
Mur ligases (MurC-MurF), a group of bacterial enzymes that catalyze four consecutive steps in the formation of cytoplasmic peptidoglycan precursor, are becoming increasingly adopted as targets in antibacterial drug design. Based on the crystal structure of MurD cocrystallized with thiazolidine-2,4-dione inhibitor I, we have designed, synthesized, and evaluated a series of improved glutamic acid containing 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD with IC(50) values up to 28 μM. Inhibitor 37, with an IC(50) of 34 μM, displays a weak antibacterial activity against S. aureus ATCC 29213 and E. faecalis ATCC 29212 with minimal inhibitory concentrations of 128 μg/mL. High-resolution crystal structures of MurD in complex with two new inhibitors (compounds 23 and 51) reveal details of their binding modes within the active site and provide valuable information for further structure-based optimization.
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Affiliation(s)
- Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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91
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Höfer I, Crüsemann M, Radzom M, Geers B, Flachshaar D, Cai X, Zeeck A, Piel J. Insights into the biosynthesis of hormaomycin, an exceptionally complex bacterial signaling metabolite. ACTA ACUST UNITED AC 2011; 18:381-91. [PMID: 21439483 DOI: 10.1016/j.chembiol.2010.12.018] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/26/2010] [Accepted: 12/02/2010] [Indexed: 11/19/2022]
Abstract
Hormaomycin produced by Streptomyces griseoflavus is a structurally highly modified depsipeptide that contains several unique building blocks with cyclopropyl, nitro, and chlorine moieties. Within the genus Streptomyces, it acts as a bacterial hormone that induces morphological differentiation and the production of bioactive secondary metabolites. In addition, hormaomycin is an extremely potent narrow-spectrum antibiotic. In this study, we shed light on hormaomycin biosynthesis by a combination of feeding studies, isolation of the biosynthetic nonribosomal peptide synthetase (NRPS) gene cluster, and in vivo and in vitro functional analysis of enzymes. In addition, several nonnatural hormaomycin congeners were generated by feeding-induced metabolic rerouting. The NRPS contains numerous highly repetitive regions that suggest an evolutionary scenario for this unusual bacterial hormone, providing new opportunities for evolution-inspired metabolic engineering of novel nonribosomal peptides.
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Affiliation(s)
- Ivonne Höfer
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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92
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Felnagle EA, Podevels AM, Barkei JJ, Thomas MG. Mechanistically distinct nonribosomal peptide synthetases assemble the structurally related antibiotics viomycin and capreomycin. Chembiochem 2011; 12:1859-67. [PMID: 21739558 DOI: 10.1002/cbic.201100193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Elizabeth A Felnagle
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Das D, Hervé M, Feuerhelm J, Farr CL, Chiu HJ, Elsliger MA, Knuth MW, Klock HE, Miller MD, Godzik A, Lesley SA, Deacon AM, Mengin-Lecreulx D, Wilson IA. Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein. PLoS One 2011; 6:e17624. [PMID: 21445265 PMCID: PMC3060825 DOI: 10.1371/journal.pone.0017624] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/03/2011] [Indexed: 11/18/2022] Open
Abstract
Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.
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Affiliation(s)
- Debanu Das
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Mireille Hervé
- Université Paris-Sud, Laboratoire des Enveloppes Bactériennes et Antibiotiques, Orsay, France
- Centre National de la Recherche Scientifique, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Orsay, France
| | - Julie Feuerhelm
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Carol L. Farr
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Marc-André Elsliger
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Mark W. Knuth
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Heath E. Klock
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Mitchell D. Miller
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Adam Godzik
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Center for Research in Biological Systems, University of California San Diego, La Jolla, California, United States of America
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Scott A. Lesley
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ashley M. Deacon
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, United States of America
| | - Dominique Mengin-Lecreulx
- Université Paris-Sud, Laboratoire des Enveloppes Bactériennes et Antibiotiques, Orsay, France
- Centre National de la Recherche Scientifique, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Orsay, France
| | - Ian A. Wilson
- Joint Center for Structural Genomics (http://www.jcsg.org)
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
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94
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Gao X, Chooi YH, Ames BD, Wang P, Walsh CT, Tang Y. Fungal indole alkaloid biosynthesis: genetic and biochemical investigation of the tryptoquialanine pathway in Penicillium aethiopicum. J Am Chem Soc 2011; 133:2729-41. [PMID: 21299212 PMCID: PMC3045477 DOI: 10.1021/ja1101085] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tremorgenic mycotoxins are a group of indole alkaloids which include the quinazoline-containing tryptoquivaline (2) that are capable of eliciting intermittent or sustained tremors in vertebrate animals. The biosynthesis of this group of bioactive compounds, which are characterized by an acetylated quinazoline ring connected to a 6-5-5 imidazoindolone ring system via a 5-membered spirolactone, has remained uncharacterized. Here, we report the identification of a gene cluster (tqa) from P. aethiopicum that is involved in the biosynthesis of tryptoquialanine (1), which is structurally similar to 2. The pathway has been confirmed to go through an intermediate common to the fumiquinazoline pathway, fumiquinazoline F, which originates from a fungal trimodular nonribosomal peptide synthetase (NRPS). By systematically inactivating every biosynthetic gene in the cluster, followed by isolation and characterization of the intermediates, we were able to establish the biosynthetic sequence of the pathway. An unusual oxidative opening of the pyrazinone ring by an FAD-dependent berberine bridge enzyme-like oxidoreductase has been proposed based on genetic knockout studies. Notably, a 2-aminoisobutyric acid (AIB)-utilizing NRPS module has been identified and reconstituted in vitro, along with two putative enzymes of unknown functions that are involved in the synthesis of the unnatural amino acid by genetic analysis. This work provides new genetic and biochemical insights into the biosynthesis of this group of fungal alkaloids, including the tremorgens related to 2.
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Affiliation(s)
- Xue Gao
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
| | - Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
| | - Brian D. Ames
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
| | - Peng Wang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
| | - Christopher T. Walsh
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095
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95
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Kraas FI, Helmetag V, Wittmann M, Strieker M, Marahiel MA. Functional dissection of surfactin synthetase initiation module reveals insights into the mechanism of lipoinitiation. ACTA ACUST UNITED AC 2011; 17:872-80. [PMID: 20797616 DOI: 10.1016/j.chembiol.2010.06.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 06/01/2010] [Accepted: 06/03/2010] [Indexed: 11/18/2022]
Abstract
Although the N-terminally attached fatty acids are key structural elements of nonribosomally assembled lipopeptide antibiotics, little is known about the mechanism of lipid transfer during the initial step of biosynthesis. In this study, we investigated the activity of the dissected initiation module (C-A(Glu)-PCP) of surfactin synthetase SrfAA in vitro to gain further insights into the lipoinitiation reaction. The dissected condensation (C) domain catalyzes the transfer of CoA-activated 3-hydroxy fatty acid with high substrate specificity at its donor site to the peptidyl carrier protein (PCP) bound amino acid glutamate (Glu(1)). Additionally, biochemical studies on four putative acyl CoA ligases in Bacillus subtilis revealed that two of them activate 3-hydroxy fatty acids for surfactin biosynthesis in vitro and that the disruption of corresponding genes has a significant influence on surfactin production.
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Affiliation(s)
- Femke I Kraas
- Department of Chemistry, Biochemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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96
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Abstract
Natural product biosynthetic pathways have evolved enzymes with myriad activities that represent an expansive array of chemical transformations for constructing secondary metabolites. Recently, harnessing the biosynthetic potential of these enzymes through chemoenzymatic synthesis has provided a powerful tool that often rivals the most sophisticated methodologies in modern synthetic chemistry and provides new opportunities for accessing chemical diversity. Herein, we describe our research efforts with enzymes from a broad collection of biosynthetic systems, highlighting recent progress in this exciting field.
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Affiliation(s)
- Jonathan D. Mortison
- Life Sciences Institute, Department of Chemistry and Department of Medicinal Chemistry, 210 Washtenaw Avenue, University of Michigan, Ann Arbor, Michigan 48109
| | - David H. Sherman
- Life Sciences Institute, Department of Chemistry and Department of Medicinal Chemistry, 210 Washtenaw Avenue, University of Michigan, Ann Arbor, Michigan 48109
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97
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Cheng X, Lu G, Qi J, Cheng H, Gao F, Wang J, Yan J. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of SAICAR synthase from Streptococcus suis serotype 2. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:909-912. [PMID: 20693665 PMCID: PMC2917288 DOI: 10.1107/s1744309110020518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 05/29/2010] [Indexed: 05/29/2023]
Abstract
Phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICAR synthase) plays an essential role in the de novo biosynthesis of purine nucleotides. In this study, the SAICAR synthase from Streptococcus suis was cloned and overexpressed in Escherichia coli. The subsequent product was purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 2.8 A resolution and belonged to space group P2, with unit-cell parameters a=70.2, b=52.2, c=153.9 A, beta=102.8 degrees.
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Affiliation(s)
- Xia Cheng
- Key Laboratory of Environment Veterinary Science, Shanxi Agricultural University, Shanxi, People’s Republic of China
| | - Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hao Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Feng Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jundong Wang
- Key Laboratory of Environment Veterinary Science, Shanxi Agricultural University, Shanxi, People’s Republic of China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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98
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Cruz de Carvalho MH, Brunet J, Bazin J, Kranner I, d' Arcy-Lameta A, Zuily-Fodil Y, Contour-Ansel D. Homoglutathione synthetase and glutathione synthetase in drought-stressed cowpea leaves: expression patterns and accumulation of low-molecular-weight thiols. J Plant Physiol 2010; 167:480-487. [PMID: 20036031 DOI: 10.1016/j.jplph.2009.10.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/24/2009] [Accepted: 10/26/2009] [Indexed: 05/28/2023]
Abstract
Glutathione (GSH) is an abundant metabolite and a major antioxidant in plant cells. However, in the Leguminosae, homoglutathione (hGSH) may replace glutathione (GSH) partially or completely. To date, cowpea (Vigna unguiculata) has been considered a non-hGSH-producing species, and no hGSHS cDNA has been isolated. Here we report on the cloning of a full-length cDNA coding for a hGSHS (EC 6.3.2.23) and the cloning of a partial cDNA coding for a putative glutathione synthetase (GSHS; EC 6.3.2.3) in cowpea leaf extracts. These cDNAs possess, respectively, the leucine/proline hGSHS signature and the alanine/alanine GSHS signature at the 3' end. Expression analysis showed a significant up-regulation of hGSHS during progressive drought stress that could be directly related to the drought tolerance of the cowpea cultivar used, while GSHS was mainly constitutively expressed. Nevertheless, quantification of low-molecular-weight thiols confirmed the previous findings that cowpea is essentially a GSH producing plant, as no hGSH was detected in the leaves. These findings raise new questions regarding the function, activity and substrate specificity of the cloned hGSHS cDNA. These questions are discussed.
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99
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Fujiwara K, Maita N, Hosaka H, Okamura-Ikeda K, Nakagawa A, Taniguchi H. Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. J Biol Chem 2010; 285:9971-9980. [PMID: 20089862 PMCID: PMC2843243 DOI: 10.1074/jbc.m109.078717] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/28/2009] [Indexed: 11/06/2022] Open
Abstract
Lipoate-protein ligase A (LplA) catalyzes the attachment of lipoic acid to lipoate-dependent enzymes by a two-step reaction: first the lipoate adenylation reaction and, second, the lipoate transfer reaction. We previously determined the crystal structure of Escherichia coli LplA in its unliganded form and a binary complex with lipoic acid (Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A., and Taniguchi, H. (2005) J Biol. Chem. 280, 33645-33651). Here, we report two new LplA structures, LplA.lipoyl-5'-AMP and LplA.octyl-5'-AMP.apoH-protein complexes, which represent the post-lipoate adenylation intermediate state and the pre-lipoate transfer intermediate state, respectively. These structures demonstrate three large scale conformational changes upon completion of the lipoate adenylation reaction: movements of the adenylate-binding and lipoate-binding loops to maintain the lipoyl-5'-AMP reaction intermediate and rotation of the C-terminal domain by about 180 degrees . These changes are prerequisites for LplA to accommodate apoprotein for the second reaction. The Lys(133) residue plays essential roles in both lipoate adenylation and lipoate transfer reactions. Based on structural and kinetic data, we propose a reaction mechanism driven by conformational changes.
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Affiliation(s)
- Kazuko Fujiwara
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503.
| | - Nobuo Maita
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
| | - Harumi Hosaka
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Kazuko Okamura-Ikeda
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Hisaaki Taniguchi
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
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100
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Steinle A, Witthoff S, Krause JP, Steinbüchel A. Establishment of cyanophycin biosynthesis in Pichia pastoris and optimization by use of engineered cyanophycin synthetases. Appl Environ Microbiol 2010; 76:1062-70. [PMID: 20038708 PMCID: PMC2820970 DOI: 10.1128/aem.01659-09] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 12/12/2009] [Indexed: 11/20/2022] Open
Abstract
Two strains of the methylotrophic yeast Pichia pastoris were used to establish cyanophycin (multi-L-arginyl-poly-L-aspartic acid [CGP]) synthesis and to explore the applicability of this industrially widely used microorganism for the production of this polyamide. Therefore, the CGP synthetase gene from the cyanobacterium Synechocystis sp. strain PCC 6308 (cphA(6308)) was expressed under the control of the alcohol oxidase 1 promoter, yielding CGP contents of up to 10.4% (wt/wt), with the main fraction consisting of the soluble form of the polymer. To increase the polymer contents and to obtain further insights into the structural or catalytic properties of the enzyme, site-directed mutagenesis was applied to cphA(6308) and the mutated gene products were analyzed after expression in P. pastoris and Escherichia coli, respectively. CphA(6308)Delta1, which was truncated by one amino acid at the C terminus; point mutated CphA(6308)C595S; and the combined double-mutant CphA(6308)Delta1C595S protein were purified. They exhibited up to 2.5-fold higher enzyme activities of 4.95 U/mg, 3.20 U/mg, and 4.17 U/mg, respectively, than wild-type CphA(6308) (2.01 U/mg). On the other hand, CphA proteins truncated by two (CphA(6308)Delta2) or three (CphA(6308)Delta3) amino acids at the C terminus showed similar or reduced CphA enzyme activity in comparison to CphA(6308). In flask experiments, a maximum of 14.3% (wt/wt) CGP was detected after the expression of CphA(6308)Delta1 in P. pastoris. For stabilization of the expression plasmid, the his4 gene from Saccharomyces cerevisiae was cloned into the expression vector used and the constructs were transferred to histidine auxotrophic P. pastoris strain GS115. Parallel fermentations at a one-to-one scale revealed 26 degrees C and 6.0 as the optimal temperature and pH, respectively, for CGP synthesis. After optimization of fermentation parameters, medium composition, and the length of the cultivation period, CGP contents could be increased from 3.2 to 13.0% (wt/wt) in cells of P. pastoris GS115 expressing CphA(6308) and up to even 23.3% (wt/wt) in cells of P. pastoris GS115 expressing CphA(6308)Delta1.
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Affiliation(s)
- Anna Steinle
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Sabrina Witthoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Jens P. Krause
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Germany
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