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Enhanced Rishirilide Biosynthesis by a Rare In-Cluster Phosphopantetheinyl Transferase in Streptomyces xanthophaeus. Microbiol Spectr 2022; 10:e0324722. [PMID: 36326495 PMCID: PMC9769936 DOI: 10.1128/spectrum.03247-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Phosphopantetheinyl transferases (PPTases) play important roles in activating apo-acyl carrier proteins (apo-ACPs) and apo-peptidyl carrier proteins (apo-PCPs) in both primary and secondary metabolism. PPTases catalyze the posttranslational modifications of those carrier proteins by covalent attachment of the 4'-phosphopantetheine group to a conserved serine residue. The protein-protein interactions between a PPTase and a cognate acyl or peptidyl carrier protein have important regulatory functions in microbial biosynthesis, but the molecular mechanism underlying their specific recognition remains elusive. In this study, we identified a new rishirilide biosynthetic gene cluster with a rare in-cluster PPTase from Streptomyces xanthophaeus no2. The function of this Sfp-type PPTase, SxrX, in rishirilide production was confirmed using genetic mutagenesis and biochemical characterization. We applied molecular modeling and site-directed mutagenesis to identify key residues mediating the protein-protein interaction between SxrX and its cognate ACP. In addition, six natural products were isolated from wild-type S. xanthophaeus no2 and the ΔsxrX mutant, including rishirilide A and lupinacidin A, that exhibited antimicrobial and anticancer activities, respectively. SxrX is the first Sfp-type PPTase identified from an aromatic polyketide biosynthetic gene cluster and shown to be responsible for high-level production of rishirilide derivatives. IMPORTANCE Genome mining has been a vital means for natural product drug discovery in the postgenomic era. The rishirilide-type polyketides have attracted attention due to their potent bioactivity, but the poor robustness of production hosts has limited further research and development. This study not only identifies a hyperproducer of rishirilides but also reveals a rare, in-cluster PPTase SxrX that plays an important role in boosting rishirilide biosynthesis. Experimental and computational investigations revealed new insights on the protein-protein interaction between SxrX and its cognate ACP with wide implications for understanding polyketide biosynthesis.
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2
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Bhatia I, Yadav S, Biswal BK. Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously. Acta Crystallogr F Struct Biol Commun 2022; 78:252-264. [DOI: 10.1107/s2053230x22005738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/26/2022] [Indexed: 11/11/2022] Open
Abstract
The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the structure of the target protein by the molecular-replacement method no convincing solutions were obtained, indicating that the diffraction data may correspond to a crystal of an artifactual protein, which was finally identified by the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) server. The msAcpS structure was solved at 2.27 Å resolution and structural analysis showed an overall conserved fold. msAcpS formed a trimeric structure similar to those of other reported structures of AcpS from various organisms; however, the residues involved in trimer formation are not strictly conserved. An unrelated metal ion (Ni2+), which was possibly incorporated during protein purification, was observed in the proximity of His49 and His116. Structural and sequence differences were observed in the loop connecting the α3 and α4 helices that is responsible for the open and closed conformations of the enzyme. Moreover, the structural analysis of msAcpS augments the current understanding of this enzyme, which plays a crucial role in the functional activation of acyl-carrier proteins in the fatty-acid biosynthesis pathway.
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3
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Zeng L, Zhong G, Huang Y, Jia J, Bi H. A phosphopantetheinyl transferase gene restricted to Porphyromonas. Res Microbiol 2022; 173:103940. [PMID: 35337986 DOI: 10.1016/j.resmic.2022.103940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Abstract
The phosphopantetheinyl transferases (PPTases) catalyze the post-translational modification of carrier proteins (CPs) from fatty acid synthases (FASs) in primary metabolism and from polyketide synthases (PKSs) and non-ribosomal polypeptide synthases (NRPSs) in secondary metabolism. Based on the conserved sequence motifs and substrate specificities, two types (AcpS-type and Sfp-type) of PPTases have been identified in prokaryotes. We present here that Porphyromonas gingivalis, the keystone pathogen in chronic periodontitis, harbors merely one PPTase, namely PptP. Complementation and gene deletion experiments clearly show that PptP can replace the function of Escherichia coli AcpS and is essential for the growth of P. gingivalis. Purified PptP transfers the 4-phosphopantetheine moiety of CoA to inactive apo-acyl carrier protein (ACP) to form holo-ACP, which functions as an active carrier of the acyl intermediates of fatty acid synthesis. Moreover, PptP exhibits broad substrate specificity, modifying all ACP substrates tested and catalyzing the transfer of coenzyme A (CoA) derivatives. The lack of sequence alignment with known PPTases together with phylogenetic analyses revealed PptP as a new class of PPTases. Identification of the new PPTase gene pptP exclusive in Porphyromonas species reveals a potential target for treating P. gingivalis infections.
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Affiliation(s)
- Liping Zeng
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Guowei Zhong
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Huang
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Jia Jia
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Hongkai Bi
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China.
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4
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Martín JF, Liras P, Sánchez S. Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes. Front Microbiol 2021; 12:630694. [PMID: 33796086 PMCID: PMC8007912 DOI: 10.3389/fmicb.2021.630694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, Mexico
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5
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Thongkawphueak T, Winter AJ, Williams C, Maple HJ, Soontaranon S, Kaewhan C, Campopiano DJ, Crump MP, Wattana-Amorn P. Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis. Biochemistry 2021; 60:219-230. [PMID: 33416314 DOI: 10.1021/acs.biochem.0c00830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The acyl carrier protein (ACP) is an indispensable component of both fatty acid and polyketide synthases and is primarily responsible for delivering acyl intermediates to enzymatic partners. At present, increasing numbers of multidomain ACPs have been discovered with roles in molecular recognition of trans-acting enzymatic partners as well as increasing metabolic flux. Further structural information is required to provide insight into their function, yet to date, the only high-resolution structure of this class to be determined is that of the doublet ACP (two continuous ACP domains) from mupirocin synthase. Here we report the solution nuclear magnetic resonance (NMR) structure of the doublet ACP domains from PigH (PigH ACP1-ACP2), which is an enzyme that catalyzes the formation of the bipyrrolic intermediate of prodigiosin, a potent anticancer compound with a variety of biological activities. The PigH ACP1-ACP2 structure shows each ACP domain consists of three conserved helices connected by a linker that is partially restricted by interactions with the ACP1 domain. Analysis of the holo (4'-phosphopantetheine, 4'-PP) form of PigH ACP1-ACP2 by NMR revealed conformational exchange found predominantly in the ACP2 domain reflecting the inherent plasticity of this ACP. Furthermore, ensemble models obtained from SAXS data reveal two distinct conformers, bent and extended, of both apo (unmodified) and holo PigH ACP1-ACP2 mediated by the central linker. The bent conformer appears to be a result of linker-ACP1 interactions detected by NMR and might be important for intradomain communication during the biosynthesis. These results provide new insights into the behavior of the interdomain linker of multiple ACP domains that may modulate protein-protein interactions. This is likely to become an increasingly important consideration for metabolic engineering in prodigiosin and other related biosynthetic pathways.
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Affiliation(s)
- Thitapa Thongkawphueak
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ashley J Winter
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Christopher Williams
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, Centre for Synthetic Biology Research, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, U.K
| | - Hannah J Maple
- School of Social and Community Medicine, University of Bristol, Oakfield House, Bristol BS8 2BN, U.K
| | - Siriwat Soontaranon
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | - Chonthicha Kaewhan
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | - Dominic J Campopiano
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, Centre for Synthetic Biology Research, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, U.K
| | - Pakorn Wattana-Amorn
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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6
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Enhancement of fatty acid biosynthesis by exogenous acetyl-CoA carboxylase and pantothenate kinase in Escherichia coli. Biotechnol Lett 2020; 42:2595-2605. [DOI: 10.1007/s10529-020-02996-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/01/2020] [Indexed: 01/25/2023]
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7
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Canestrari MJ, Serrano B, Bartoli J, Prima V, Bornet O, Puppo R, Bouveret E, Guerlesquin F, Viala JP. Deciphering the specific interaction between the acyl carrier protein IacP and the T3SS‐major hydrophobic translocator SipB from
Salmonella. FEBS Lett 2019; 594:251-265. [DOI: 10.1002/1873-3468.13593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/13/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Mickaël J. Canestrari
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Bastien Serrano
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Julia Bartoli
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Valérie Prima
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Olivier Bornet
- NMR Platform Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Rémy Puppo
- Proteomics Platform‐ IBISA2 Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Emmanuelle Bouveret
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Françoise Guerlesquin
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
| | - Julie P. Viala
- LISM Institut de Microbiologie de la Méditerranée CNRS and Aix‐Marseille University France
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8
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Park J, Lee Y, Cheon D, Kim Y. Structure and dynamics of human and bacterial acyl carrier proteins and their interactions with fatty acid synthesis proteins. Biochem Biophys Res Commun 2019; 516:1183-1189. [PMID: 31296387 DOI: 10.1016/j.bbrc.2019.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 07/05/2019] [Indexed: 11/17/2022]
Abstract
Acyl carrier protein (ACP) is highly conserved across taxa and plays key roles in the fatty acid synthesis system by mediating acyl group delivery and shuttling. Here, we compared the structural and dynamic features of human type Ι ACP (hACP) and Escherichia coli type II ACP (EcACP). Analysis of chemical shift perturbations upon octanoyl group attachment showed perturbations in hACP only near acyl-group attachment sites, whereas EcACP showed the perturbation at residues in the hydrophobic cavity. This difference confirmed that hACP does not sequester the acyl chain in the hydrophobic cavity, which is blocked by hydrophobic triad residues (L34, L39, and V64). Moreover, hACP showed more flexible backbone dynamics than EcACP, especially in the front of α1α2 loop. We further investigated the interactions of hACP with Streptomyces coelicolor ACP synthase (ScAcpS), which is used to convert apo mammalian ACP to the holo form. Similar to protein-protein interface (PPI) found in hACP-hAcpS crystal structure, docking simulation and binding affinity measurements showed that the hydrophobic residues in universal recognition helix II of hACP contribute mainly to ScAcpS binding with binding affinity of 9.2 ± 9.1 × 104 M. In contrast, interaction found in EcACP-EcAcpS crystal structure is dominated by electrostatic interactions. These results suggest that ScAcpS has relatively relaxed substrate specificity and a similar charge distribution to hAcpS. These fundamental differences of the charge distribution in hAcpS, ScAcpS and EcAcpS largely affect the interaction with hACP. These findings can provide a useful resource for development of novel antibiotics inhibiting PPI in bacterial FAS proteins with specificity.
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Affiliation(s)
- Jungwoo Park
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Yeongjoon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Dasom Cheon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea.
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9
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Tallorin L, Wang J, Kim WE, Sahu S, Kosa NM, Yang P, Thompson M, Gilson MK, Frazier PI, Burkart MD, Gianneschi NC. Discovering de novo peptide substrates for enzymes using machine learning. Nat Commun 2018; 9:5253. [PMID: 30531862 PMCID: PMC6286390 DOI: 10.1038/s41467-018-07717-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/14/2018] [Indexed: 01/22/2023] Open
Abstract
The discovery of peptide substrates for enzymes with exclusive, selective activities is a central goal in chemical biology. In this paper, we develop a hybrid computational and biochemical method to rapidly optimize peptides for specific, orthogonal biochemical functions. The method is an iterative machine learning process by which experimental data is deposited into a mathematical algorithm that selects potential peptide substrates to be tested experimentally. Once tested, the algorithm uses the experimental data to refine future selections. This process is repeated until a suitable set of de novo peptide substrates are discovered. We employed this technology to discover orthogonal peptide substrates for 4’-phosphopantetheinyl transferase, an enzyme class that covalently modifies proteins. In this manner, we have demonstrated that machine learning can be leveraged to guide peptide optimization for specific biochemical functions not immediately accessible by biological screening techniques, such as phage display and random mutagenesis. The discovery of peptide substrates for enzymes with selective activities is a central goal in chemical biology. Here, the authors develop a hybrid method combining machine learning and experimental testing for fast optimization of peptides for specific, orthogononal functions.
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Affiliation(s)
- Lorillee Tallorin
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - JiaLei Wang
- School of Operations Research and Information Engineering, Cornell University, 232 Rhodes Hall, Ithaca, NY, 14853-3801, USA
| | - Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Swagat Sahu
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Nicolas M Kosa
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Pu Yang
- School of Operations Research and Information Engineering, Cornell University, 232 Rhodes Hall, Ithaca, NY, 14853-3801, USA
| | - Matthew Thompson
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Chemistry, Department of Materials Science and Engineering, Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Peter I Frazier
- School of Operations Research and Information Engineering, Cornell University, 232 Rhodes Hall, Ithaca, NY, 14853-3801, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.
| | - Nathan C Gianneschi
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA. .,Department of Chemistry, Department of Materials Science and Engineering, Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
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10
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Marcella AM, Culbertson SJ, Shogren-Knaak MA, Barb AW. Structure, High Affinity, and Negative Cooperativity of the Escherichia coli Holo-(Acyl Carrier Protein):Holo-(Acyl Carrier Protein) Synthase Complex. J Mol Biol 2017; 429:3763-3775. [DOI: 10.1016/j.jmb.2017.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/08/2017] [Accepted: 10/11/2017] [Indexed: 01/01/2023]
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11
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Characterization of Discrete Phosphopantetheinyl Transferases in Streptomyces tsukubaensis L19 Unveils a Complicate Phosphopantetheinylation Network. Sci Rep 2016; 6:24255. [PMID: 27052100 PMCID: PMC4823652 DOI: 10.1038/srep24255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/23/2016] [Indexed: 11/08/2022] Open
Abstract
Phosphopantetheinyl transferases (PPTases) play essential roles in both primary metabolisms and secondary metabolisms via post-translational modification of acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs). In this study, an industrial FK506 producing strain Streptomyces tsukubaensis L19, together with Streptomyces avermitilis, was identified to contain the highest number (five) of discrete PPTases known among any species thus far examined. Characterization of the five PPTases in S. tsukubaensis L19 unveiled that stw ACP, an ACP in a type II PKS, was phosphopantetheinylated by three PPTases FKPPT1, FKPPT3, and FKACPS; sts FAS ACP, the ACP in fatty acid synthase (FAS), was phosphopantetheinylated by three PPTases FKPPT2, FKPPT3, and FKACPS; TcsA-ACP, an ACP involved in FK506 biosynthesis, was phosphopantetheinylated by two PPTases FKPPT3 and FKACPS; FkbP-PCP, an PCP involved in FK506 biosynthesis, was phosphopantetheinylated by all of these five PPTases FKPPT1-4 and FKACPS. Our results here indicate that the functions of these PPTases complement each other for ACPs/PCPs substrates, suggesting a complicate phosphopantetheinylation network in S. tsukubaensis L19. Engineering of these PPTases in S. tsukubaensis L19 resulted in a mutant strain that can improve FK506 production.
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12
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Wang YY, Zhang XS, Ren NN, Guo YY, Jiang XH, Jiang H, Li YD, Li YQ. Two bacterial group II phosphopantetheinyl transferases involved in both primary metabolism and secondary metabolism. Curr Microbiol 2014; 70:390-7. [PMID: 25413605 DOI: 10.1007/s00284-014-0735-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
Abstract
It is known that bacterial group II phosphopantetheinyl transferases (PPTases) usually phosphopantetheinylate acyl carrier proteins (ACPs) involved in the secondary metabolism. For example, a bacterial group II PPTase SchPPT has been known to phosphopantetheinylate only ACPs involved in secondary metabolism, such as scn ACP0-2 and scn ACP7. In this study, we found two bacterial group II PPTases, Hppt and Sppt, could phosphopantetheinylate not only scn ACP0-2 and scn ACP7, but also sch FAS ACP, an ACP involved in primary metabolism. Swapping of the N terminus and C terminus of PPTases showed that (i) both the hybrids Hppt-Sppt and Sppt-Hppt could phosphopantetheinylate sch FAS ACP but not scn ACP0-2; (ii) both the hybrids Sppt-SchPPT and SchPPT-Sppt lost abilities to phosphopantetheinylate sch FAS ACP and scn ACP0-2. Hppt and Sppt represent group II PPTases which phosphopantetheinylate both ACPs involved in primary metabolism and ACPs involved in secondary metabolism.
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Affiliation(s)
- Yue-Yue Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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13
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Kotowska M, Pawlik K. Roles of type II thioesterases and their application for secondary metabolite yield improvement. Appl Microbiol Biotechnol 2014; 98:7735-46. [PMID: 25081554 PMCID: PMC4147253 DOI: 10.1007/s00253-014-5952-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 12/31/2022]
Abstract
A large number of antibiotics and other industrially important microbial secondary metabolites are synthesized by polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). These multienzymatic complexes provide an enormous flexibility in formation of diverse chemical structures from simple substrates, such as carboxylic acids and amino acids. Modular PKSs and NRPSs, often referred to as megasynthases, have brought about a special interest due to the colinearity between enzymatic domains in the proteins working as an “assembly line” and the chain elongation and modification steps. Extensive efforts toward modified compound biosynthesis by changing organization of PKS and NRPS domains in a combinatorial manner laid good grounds for rational design of new structures and their controllable biosynthesis as proposed by the synthetic biology approach. Despite undeniable progress made in this field, the yield of such “unnatural” natural products is often not satisfactory. Here, we focus on type II thioesterases (TEIIs)—discrete hydrolytic enzymes often encoded within PKS and NRPS gene clusters which can be used to enhance product yield. We review diverse roles of TEIIs (removal of aberrant residues blocking the megasynthase, participation in substrate selection, intermediate, and product release) and discuss their application in new biosynthetic systems utilizing PKS and NRPS parts.
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Affiliation(s)
- Magdalena Kotowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Rudolfa Weigla 12, 53-114, Wroclaw, Poland,
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14
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Wang YY, Li YD, Liu JB, Ran XX, Guo YY, Ren NN, Chen X, Jiang H, Li YQ. Characterization and evolutionary implications of the triad Asp-Xxx-Glu in group II phosphopantetheinyl transferases. PLoS One 2014; 9:e103031. [PMID: 25036863 PMCID: PMC4103896 DOI: 10.1371/journal.pone.0103031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/25/2014] [Indexed: 01/11/2023] Open
Abstract
Phosphopantetheinyl transferases (PPTases), which play an essential role in both primary and secondary metabolism, are magnesium binding enzymes. In this study, we characterized the magnesium binding residues of all known group II PPTases by biochemical and evolutionary analysis. Our results suggested that group II PPTases could be classified into two subgroups, two-magnesium-binding-residue-PPTases containing the triad Asp-Xxx-Glu and three-magnesium-binding-residue-PPTases containing the triad Asp-Glu-Glu. Mutations of two three-magnesium-binding-residue-PPTases and one two-magnesium-binding-residue-PPTase indicate that the first and the third residues in the triads are essential to activities; the second residues in the triads are non-essential. Although variations of the second residues in the triad Asp-Xxx-Glu exist throughout the whole phylogenetic tree, the second residues are conserved in animals, plants, algae, and most prokaryotes, respectively. Evolutionary analysis suggests that: the animal group II PPTases may originate from one common ancestor; the plant two-magnesium-binding-residue-PPTases may originate from one common ancestor; the plant three-magnesium-binding-residue-PPTases may derive from horizontal gene transfer from prokaryotes.
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Affiliation(s)
- Yue-Yue Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu-Dong Li
- Department of Bioengineering, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Jian-Bo Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin-Xin Ran
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuan-Yang Guo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ni-Ni Ren
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hui Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang, China
- * E-mail: (HJ); (YQL)
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang, China
- * E-mail: (HJ); (YQL)
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15
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Beld J, Sonnenschein EC, Vickery CR, Noel JP, Burkart MD. The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. Nat Prod Rep 2014; 31:61-108. [PMID: 24292120 PMCID: PMC3918677 DOI: 10.1039/c3np70054b] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: up to 2013. Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from identification, characterization, structure determination, mutagenesis, inhibition, and engineering in synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of enzymes that post-translationally install a 4'-phosphopantetheine arm on various carrier proteins.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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16
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Halavaty AS, Kim Y, Minasov G, Shuvalova L, Dubrovska I, Winsor J, Zhou M, Onopriyenko O, Skarina T, Papazisi L, Kwon K, Peterson SN, Joachimiak A, Savchenko A, Anderson WF. Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1359-70. [PMID: 22993090 PMCID: PMC3447402 DOI: 10.1107/s0907444912029101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 06/26/2012] [Indexed: 05/13/2024]
Abstract
Some bacterial type II fatty-acid synthesis (FAS II) enzymes have been shown to be important candidates for drug discovery. The scientific and medical quest for new FAS II protein targets continues to stimulate research in this field. One of the possible additional candidates is the acyl-carrier-protein synthase (AcpS) enzyme. Its holo form post-translationally modifies the apo form of an acyl carrier protein (ACP), which assures the constant delivery of thioester intermediates to the discrete enzymes of FAS II. At the Center for Structural Genomics of Infectious Diseases (CSGID), AcpSs from Staphylococcus aureus (AcpS(SA)), Vibrio cholerae (AcpS(VC)) and Bacillus anthracis (AcpS(BA)) have been structurally characterized in their apo, holo and product-bound forms, respectively. The structure of AcpS(BA) is emphasized because of the two 3',5'-adenosine diphosphate (3',5'-ADP) product molecules that are found in each of the three coenzyme A (CoA) binding sites of the trimeric protein. One 3',5'-ADP is bound as the 3',5'-ADP part of CoA in the known structures of the CoA-AcpS and 3',5'-ADP-AcpS binary complexes. The position of the second 3',5'-ADP has never been described before. It is in close proximity to the first 3',5'-ADP and the ACP-binding site. The coordination of two ADPs in AcpS(BA) may possibly be exploited for the design of AcpS inhibitors that can block binding of both CoA and ACP.
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Affiliation(s)
- Andrei S. Halavaty
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, USA
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
- Computational Institute, University of Chicago, Chicago, IL 60637, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ievgeniia Dubrovska
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - James Winsor
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Min Zhou
- Center for Structural Genomics of Infectious Diseases, USA
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
- Computational Institute, University of Chicago, Chicago, IL 60637, USA
| | - Olena Onopriyenko
- Center for Structural Genomics of Infectious Diseases, USA
- University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Tatiana Skarina
- Center for Structural Genomics of Infectious Diseases, USA
- University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Leka Papazisi
- Center for Structural Genomics of Infectious Diseases, USA
- J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Keehwan Kwon
- Center for Structural Genomics of Infectious Diseases, USA
- J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Scott N. Peterson
- Center for Structural Genomics of Infectious Diseases, USA
- J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, USA
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
- Computational Institute, University of Chicago, Chicago, IL 60637, USA
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases, USA
- University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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17
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Crosby J, Crump MP. The structural role of the carrier protein--active controller or passive carrier. Nat Prod Rep 2012; 29:1111-37. [PMID: 22930263 DOI: 10.1039/c2np20062g] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Common to all FASs, PKSs and NRPSs is a remarkable component, the acyl or peptidyl carrier protein (A/PCP). These take the form of small individual proteins in type II systems or discrete folded domains in the multi-domain type I systems and are characterized by a fold consisting of three major α-helices and between 60-100 amino acids. This protein is central to these biosynthetic systems and it must bind and transport a wide variety of functionalized ligands as well as mediate numerous protein-protein interactions, all of which contribute to efficient enzyme turnover. This review covers the structural and biochemical characterization of carrier proteins, as well as assessing their interactions with different ligands, and other synthase components. Finally, their role as an emerging tool in biotechnology is discussed.
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Affiliation(s)
- John Crosby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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18
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Neves MAC, Yeager M, Abagyan R. Unusual arginine formations in protein function and assembly: rings, strings, and stacks. J Phys Chem B 2012; 116:7006-13. [PMID: 22497303 DOI: 10.1021/jp3009699] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interfaces are often stabilized by a small number of dominant contacts, exemplified by the overrepresentation of arginine residues at oligomerization interfaces. Positively charged arginines are most commonly involved in ion pairs of opposite charge; however, previous work of Scheraga and co-workers described the stable, close range interaction between guanidinium pairs in a solvated environment. To extend this work, we searched over 70 thousand protein structures and complexes for unusual formations of arginine residues supported by the electron density. Symmetry transformations were used to generate full assemblies. Clusters of four to eight arginine residues with C(ζ)-C(ζ) distances <5 Å, organized as rings with four to eight members, stacks of two arginines, and strings of stacked arginines, are commonly located at the interfaces of oligomeric proteins. The positive charge is properly balanced by negatively charged counterions in about 90% of the cases. We also observed planar stacking of guanidinium groups, bridged by hydrogen bonds and interactions with water molecules. The guanidinium groups are commonly involved in five hydrogen bonds with water molecules and acceptor groups from surrounding amino acids. Water molecules have a bridging effect on the arginine pairs, but in some cases, small molecular weight chemicals in the crystallization buffer may be misinterpreted as water molecules. In summary, despite electrostatic repulsion, arginines do form various clusters that are exposed to interact with and potentially be controlled or switched by charged metabolites, membrane lipids, nucleic acids, or side chains of other proteins. Control of the stability of arginine clusters may play an important role in protein-protein oligomerization, molecular recognition, and ligand binding.
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Affiliation(s)
- Marco A C Neves
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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