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Reynolds JA, Vishweshwaraiah YL, Chirasani VR, Pritchard JR, Dokholyan NV. An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity. J Biol Chem 2023; 299:103069. [PMID: 36841477 PMCID: PMC10060751 DOI: 10.1016/j.jbc.2023.103069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal efforts to exert tight and reversible control over their activity for various biotechnological applications. Here, we apply a rational, computation-guided methodology to design and test a transferase-class enzyme allosterically regulated by light-oxygen-voltage 2 sensing domain. We utilize computational techniques to determine the intrinsic allosteric networks within N-acyltransferase (Orf11/∗Dbv8) and identify potential allosteric sites on the protein's surface. We insert light-oxygen-voltage 2 sensing domain at the predicted allosteric site, exerting reversible control over enzymatic activity. We demonstrate blue-light regulation of N-acyltransferase (Orf11/∗Dbv8) function. Our study for the first time demonstrates optogenetic regulation of a transferase-class enzyme as a proof-of-concept for controllable transferase design. This successful design opens the door for many future applications in metabolic engineering and cellular programming.
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Affiliation(s)
- J A Reynolds
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Y L Vishweshwaraiah
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - V R Chirasani
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - J R Pritchard
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - N V Dokholyan
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA; Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA; Department of Chemistry, Penn State University, University Park, Pennsylvania, USA.
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2
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Tian L, Shi S, Zhang X, Han F, Dong H. Newest perspectives of glycopeptide antibiotics: biosynthetic cascades, novel derivatives, and new appealing antimicrobial applications. World J Microbiol Biotechnol 2023; 39:67. [PMID: 36593427 PMCID: PMC9807434 DOI: 10.1007/s11274-022-03512-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Glycopeptide antibiotics (GPAs) are a family of non-ribosomal peptide natural products with polypeptide skeleton characteristics, which are considered the last resort for treating severe infections caused by multidrug-resistant Gram-positive pathogens. Over the past few years, an increasing prevalence of Gram-positive resistant strain "superbugs" has emerged. Therefore, more efforts are needed to study and modify the GPAs to overcome the challenge of superbugs. In this mini-review, we provide an overview of the complex biosynthetic gene clusters (BGCs), the ingenious crosslinking and tailoring modifications, the new GPA derivatives, the discoveries of new natural GPAs, and the new applications of GPAs in antivirus and anti-Gram-negative bacteria. With the development and interdisciplinary integration of synthetic biology, next-generation sequencing (NGS), and artificial intelligence (AI), more GPAs with new chemical structures and action mechanisms will constantly be emerging.
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Affiliation(s)
- Li Tian
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Shi Shi
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Xiangmei Zhang
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Fubo Han
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Huijun Dong
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
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3
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Xia TY, Chen XA, Liu YQ, Scharf DH, Zhao QW, Li YQ. Redirection of acyl donor metabolic flux for lipopeptide A40926B0 biosynthesis. Microb Biotechnol 2022; 15:1852-1866. [PMID: 35213090 PMCID: PMC9151331 DOI: 10.1111/1751-7915.14021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/13/2022] [Accepted: 02/13/2022] [Indexed: 11/30/2022] Open
Abstract
The metabolic flux of fatty acyl‐CoAs determines lipopeptide biosynthesis efficiency, because acyl donor competition often occurs from polyketide biosynthesis and homologous pathways. We used A40926B0 as a model to investigate this mechanism. The lipopeptide A40926B0 with a fatty acyl group is the active precursor of dalbavancin, which is considered as a new lipoglycopeptide antibiotic. The biosynthetic pathway of fatty acyl‐CoAs in the A40926B0 producer Nonomuraea gerenzanensis L70 was efficiently engineered using endogenous replicon CRISPR (erCRISPR). A polyketide pathway and straight‐chain fatty acid biosynthesis were identified as major competitors in the malonyl‐CoA pool. Therefore, we modified both pathways to concentrate acyl donors for the production of the desired compound. Combined with multiple engineering approaches, including blockage of an acetylation side reaction, overexpression of acetyl‐CoA carboxylase, duplication of the dbv gene cluster and optimization of the fermentation parameters, the final strain produced 702.4 mg l‐1 of A40926B0, a 2.66‐fold increase, and the ratio was increased from 36.2% to 81.5%. Additionally, an efficient erCRISPR‐Cas9 editing system based on an endogenous replicon was specifically developed for L70, which increased conjugation efficiency by 660% and gene‐editing efficiency was up to 90%. Our strategy of redirecting acyl donor metabolic flux can be widely adopted for the metabolic engineering of lipopeptide biosynthesis.
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Affiliation(s)
- Tian-Yu Xia
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Yan-Qiu Liu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Daniel H Scharf
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
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4
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Rivas CE, Alvarado-Monzon JC, Gonzalez-Garcia G, Jimenez-Halla JOC, Rangel-Garcia J, Cristobal C, Lopez JA. Oxidative Coordination versus C 3 -C(O)Me Bond Cleavage in Acetylacetonate Iridium Complexes. Chemistry 2021; 27:8468-8472. [PMID: 33880825 DOI: 10.1002/chem.202100709] [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: 02/26/2021] [Indexed: 11/08/2022]
Abstract
Iridabicycles [Ir{κ3 -N,C,O-(pyC(H)=C(C(O)Me)2 }(Cl)(L-L)](L-L=cod (cod=1,5-cyclooctadiene), 1 a; bipy (bipy=2,2'-bipyridine), 1 b) have been obtained by oxidative coordination of 3-(pyridine-2-yl-methylene)pentane-2,4-dione L1, to the complexes [{Ir(μ-Cl)(cod)}2 ] and [{Ir(μ-Cl)(coe)2 }2 ] (coe=cis-cyclooctene), the latter in the presence of bipy. Remarkably, cleavage of the C3 -C(O)Me bond of L1 has instead been achieved in the reaction with [Ir(Cl)(dmb)2 ] (dmb=2,3-dimethylbutadiene), yielding a compound formulated as [Ir{κ2 -N,C-(pyC(H)C(C(O)Me))}(CO)(μ-Cl)(Me)]2 , 2. Treatment of dimer 2 with DMSO or PMe3 produced the complexes[Ir{κ2 -N,C-(pyC(H)C(C(O)Me)}(CO)Cl(Me)L] (L=DMSO, 3 a; PMe3 , 3 b). Plausible mechanisms for the reactions leading to complexes 1 and 2 are proposed by means of DFT calculations.
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Affiliation(s)
- Christopher E Rivas
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Campus Noria Alta. Noria Alta s/n, Guanajuato, C.P., 36050, Gto., México
| | - Jose C Alvarado-Monzon
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Campus Noria Alta. Noria Alta s/n, Guanajuato, C.P., 36050, Gto., México
| | - Gerardo Gonzalez-Garcia
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Campus Noria Alta. Noria Alta s/n, Guanajuato, C.P., 36050, Gto., México
| | - J Oscar C Jimenez-Halla
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Campus Noria Alta. Noria Alta s/n, Guanajuato, C.P., 36050, Gto., México
| | - Jesus Rangel-Garcia
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Campus Noria Alta. Noria Alta s/n, Guanajuato, C.P., 36050, Gto., México
| | - Crispin Cristobal
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Campus Noria Alta. Noria Alta s/n, Guanajuato, C.P., 36050, Gto., México
| | - Jorge A Lopez
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Campus Noria Alta. Noria Alta s/n, Guanajuato, C.P., 36050, Gto., México
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Adhikari K, Lo IW, Chen CL, Wang YL, Lin KH, Zadeh SM, Rattinam R, Li YS, Wu CJ, Li TL. Chemoenzymatic Synthesis and Biological Evaluation for Bioactive Molecules Derived from Bacterial Benzoyl Coenzyme A Ligase and Plant Type III Polyketide Synthase. Biomolecules 2020; 10:biom10050738. [PMID: 32397467 PMCID: PMC7277991 DOI: 10.3390/biom10050738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022] Open
Abstract
Plant type III polyketide synthases produce diverse bioactive molecules with a great medicinal significance to human diseases. Here, we demonstrated versatility of a stilbene synthase (STS) from Pinus Sylvestris, which can accept various non-physiological substrates to form unnatural polyketide products. Three enzymes (4-coumarate CoA ligase, malonyl-CoA synthetase and engineered benzoate CoA ligase) along with synthetic chemistry was practiced to synthesize starter and extender substrates for STS. Of these, the crystal structures of benzoate CoA ligase (BadA) from Rhodopseudomonas palustris in an apo form or in complex with a 2-chloro-1,3-thiazole-5-carboxyl-AMP or 2-methylthiazole-5-carboxyl-AMP intermediate were determined at resolutions of 1.57 Å, 1.7 Å, and 2.13 Å, respectively, which reinforces its capacity in production of unusual CoA starters. STS exhibits broad substrate promiscuity effectively affording structurally diverse polyketide products. Seven novel products showed desired cytotoxicity against a panel of cancer cell lines (A549, HCT116, Cal27). With the treatment of two selected compounds, the cancer cells underwent cell apoptosis in a dose-dependent manner. The precursor-directed biosynthesis alongside structure-guided enzyme engineering greatly expands the pharmaceutical repertoire of lead compounds with promising/enhanced biological activities.
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Affiliation(s)
- Kamal Adhikari
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - I-Wen Lo
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Chun-Liang Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Saeid Malek Zadeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Taipei 11529, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Rajesh Rattinam
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Taipei 11529, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 20224, Taiwan;
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Taipei 11529, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Correspondence: ; Tel.: +886-22787-1235
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Teicoplanin biosynthesis: unraveling the interplay of structural, regulatory, and resistance genes. Appl Microbiol Biotechnol 2020; 104:3279-3291. [PMID: 32076781 DOI: 10.1007/s00253-020-10436-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/26/2020] [Accepted: 02/04/2020] [Indexed: 01/10/2023]
Abstract
Teicoplanin (Tcp) is a clinically relevant glycopeptide antibiotic (GPA) that is produced by the actinobacterium Actinoplanes teichomyceticus. Tcp is a front-line therapy for treating severe infections caused by multidrug-resistant Gram-positive pathogens in adults and infants. In this review, we provide a detailed overview of how Tcp is produced by A. teichomyceticus by describing Tcp biosynthesis, regulation, and resistance. We summarize the knowledge gained from in vivo and in vitro studies to provide an integrated model of teicoplanin biosynthesis. Then, we discuss genetic and nutritional factors that contribute to the regulation of teicoplanin biosynthesis, focusing on those that have been successfully applied for improving teicoplanin production. A current view on teicoplanin self-resistance mechanisms in A. teichomyceticus is given, and we compare the Tcp biosynthetic gene cluster with other glycopeptide gene clusters from actinoplanetes and from unidentified isolates/metagenomics samples. Finally, we provide an outlook for further directions in studying Tcp biosynthesis and regulation.
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Alt S, Bernasconi A, Sosio M, Brunati C, Donadio S, Maffioli SI. Toward Single-Peak Dalbavancin Analogs through Biology and Chemistry. ACS Chem Biol 2019; 14:356-360. [PMID: 30830742 DOI: 10.1021/acschembio.9b00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycopeptide antibiotics are used to treat severe multidrug resistant infections caused by Gram-positive bacteria. Dalbavancin is a second generation glycopeptide approved for human use, which is obtained from A40926, a lipoglycopeptide produced by Nonomuraea sp. ATCC39727 as a mixture of biologically active congeners mainly differing in the fatty acid chains present on the glucuronic moiety. In this study, we constructed a double mutant of the A40926 producer strain lacking dbv23, and thus defective in mannose acetylation, a feature that increases A40926 production, and lacking the acyltransferases Dbv8, and thus incapable of installing the fatty acid chains. The double mutant afforded the desired deacyl, deacetyl A40926 intermediates, which could be converted by chemical reacylation yielding A40926 analogs with a greatly reduced number of congeners. The newly acylated analogs could then be transformed into dalbavancin analogs possessing the same in vitro properties as the approved drug.
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Affiliation(s)
- Silke Alt
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | | | - Margherita Sosio
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | | | - Stefano Donadio
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
| | - Sonia I. Maffioli
- Naicons Srl, Viale Ortles 22/4, 20139 Milano, Italy
- KtedoGen Srl, Viale Ortles 22/4, 20139 Milano, Italy
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8
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Huang CM, Lyu SY, Lin KH, Chen CL, Chen MH, Shih HW, Hsu NS, Lo IW, Wang YL, Li YS, Wu CJ, Li TL. Teicoplanin Reprogrammed with the N-Acyl-Glucosamine Pharmacophore at the Penultimate Residue of Aglycone Acquires Broad-Spectrum Antimicrobial Activities Effectively Killing Gram-Positive and -Negative Pathogens. ACS Infect Dis 2019; 5:430-442. [PMID: 30599088 DOI: 10.1021/acsinfecdis.8b00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipoglycopeptide antibiotics, for example, teicoplanin (Tei) and A40926, are more potent than vancomycin against Gram-positive (Gram-(+)) drug-resistant pathogens, for example, methicillin-resistant Staphylococcus aureus (MRSA). To extend their therapeutic effectiveness on vancomycin-resistant S. aureus (VRSA), the biosynthetic pathway of the N-acyl glucosamine (Glc) pharmacophore at residue 4 (r4) of teicoplanin pseudoaglycone redirection to residue 6 (r6) was attempted. On the basis of crystal structures, two regioselective biocatalysts Orf2*T (a triple-mutation mutant S98A/V121A/F193Y) and Orf11*S (a single-mutation mutant W163A) were engineered, allowing them to act on GlcNAc at r6. New analogs thereby made show marked antimicrobial activity against MRSA and VRSA by 2-3 orders of magnitude better than teicoplanin and vancomycin. The lipid side chain of the Tei-analogs armed with a terminal mono- or diguanidino group extends the antimicrobial specificity from Gram-(+) to Gram-negative (Gram-(-)), comparable to that of kanamycin. In addition to low cytotoxicity and high safety, the Tei analogs exhibit new modes of action as a result of resensitization of VRSA and Acinetobacter baumannii. The redirection of the biosynthetic pathway for the N-acyl-Glc pharmacophore from r4 to r6 bodes well for large-scale production of selected r6,Tei congeners in an environmentally friendly synthetic biology approach.
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Affiliation(s)
- Chun-Man Huang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
- Department of Microbiology and Immunology, National Yang-Ming University, 155 Linong Street, Section 2,
Beitou, Taipei 11221, Taiwan
| | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chun-Liang Chen
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Mei-Hua Chen
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Hao-Wei Shih
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - I-Wen Lo
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chang-Jer Wu
- National Taiwan Ocean University, 2 Peining Road, Jhongjhong, Keelung 20224, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
- National Chung-Hsing University, 145 Xingda Road, South Taichung 402, Taiwan
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Chan HL, Lyu L, Aw J, Zhang W, Li J, Yang HH, Hayashi H, Chiba S, Xing B. Unique Fluorescent Imaging Probe for Bacterial Surface Localization and Resistant Enzyme Imaging. ACS Chem Biol 2018; 13:1890-1896. [PMID: 29595947 DOI: 10.1021/acschembio.8b00172] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Emergence of antibiotic bacterial resistance has caused serious clinical issues worldwide due to increasingly difficult treatment. Development of a specific approach for selective visualization of resistant bacteria will be highly significant for clinical investigations to promote timely diagnosis and treatment of bacterial infections. In this article, we present an effective method that not only is able to selectively recognize drug resistant AmpC β-lactamases enzyme but, more importantly, is able to interact with bacterial cell wall components, resulting in a desired localization effect on the bacterial surface. A unique and specific enzyme-responsive cephalosporin probe (DFD-1) has been developed for the selective recognition of resistance bacteria AmpC β-lactamase, by employing fluorescence resonance energy transfer with an "off-on" bioimaging. To achieve the desired localization, a lipid-azide conjugate (LA-12) was utilized to facilitate its penetration into the bacterial surface, followed by copper-free click chemistry. This enables the probe DFD-1 to be anchored onto the cell surface. In the presence of AmpC enzymes, the cephalosporin β-lactam ring on DFD-1 will be hydrolyzed, leading to the quencher release, thus generating fluorescence for real-time resistant bacterial screening. More importantly, the bulky dibenzocyclooctyne group in DFD-1 allowed selective recognition toward the AmpC bacterial enzyme instead of its counterpart ( e.g., TEM-1 β-lactamase). Both live cell imaging and cell cytometry assays showed the great selectivity of DFD-1 to drug resistant bacterial pathogens containing the AmpC enzyme with significant fluorescence enhancement (∼67-fold). This probe presented promising capability to selectively localize and screen for AmpC resistance bacteria, providing great promise for clinical microbiological applications.
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Affiliation(s)
- Hui Ling Chan
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Linna Lyu
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Junxin Aw
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Wenmin Zhang
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Juan Li
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Huang-Hao Yang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Hirohito Hayashi
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Shunsuke Chiba
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Bengang Xing
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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Wang M, Firrman J, Zhang L, Arango-Argoty G, Tomasula P, Liu L, Xiao W, Yam K. Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus. Molecules 2017; 22:molecules22081292. [PMID: 28771188 PMCID: PMC6152273 DOI: 10.3390/molecules22081292] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 07/30/2017] [Accepted: 08/01/2017] [Indexed: 01/09/2023] Open
Abstract
Apigenin is a major dietary flavonoid with many bioactivities, widely distributed in plants. Apigenin reaches the colon region intact and interacts there with the human gut microbiota, however there is little research on how apigenin affects the gut bacteria. This study investigated the effect of pure apigenin on human gut bacteria, at both the single strain and community levels. The effect of apigenin on the single gut bacteria strains Bacteroides galacturonicus, Bifidobacterium catenulatum, Lactobacillus rhamnosus GG, and Enterococcus caccae, was examined by measuring their anaerobic growth profiles. The effect of apigenin on a gut microbiota community was studied by culturing a fecal inoculum under in vitro conditions simulating the human ascending colon. 16S rRNA gene sequencing and GC-MS analysis quantified changes in the community structure. Single molecule RNA sequencing was used to reveal the response of Enterococcus caccae to apigenin. Enterococcus caccae was effectively inhibited by apigenin when cultured alone, however, the genus Enterococcus was enhanced when tested in a community setting. Single molecule RNA sequencing found that Enterococcus caccae responded to apigenin by up-regulating genes involved in DNA repair, stress response, cell wall synthesis, and protein folding. Taken together, these results demonstrate that apigenin affects both the growth and gene expression of Enterococcus caccae.
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Affiliation(s)
- Minqian Wang
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA.
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, NJ 08901, USA.
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA.
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 114 MCB Hall, Blacksburg, VA 24060, USA.
| | - Gustavo Arango-Argoty
- Department of Computer Science, Virginia Tech, 114 MCB Hall, Blacksburg, VA 24060, USA.
| | - Peggy Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA.
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA.
| | - Weidong Xiao
- Department of Microbiology and Immunology, Temple University School of Medicine, 3400 North Broad Street, Philadelphia, PA 19140, USA.
| | - Kit Yam
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, NJ 08901, USA.
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11
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Salunke DM, Nair DT. Macromolecular structures: Quality assessment and biological interpretation. IUBMB Life 2017; 69:563-571. [DOI: 10.1002/iub.1640] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/25/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Dinakar M. Salunke
- International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi India
| | - Deepak T. Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster; 3rd Milestone, Faridabad-Gurgaon Expressway Faridabad Haryana India
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12
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Yushchuk O, Ostash B, Pham TH, Luzhetskyy A, Fedorenko V, Truman AW, Horbal L. Characterization of the Post-Assembly Line Tailoring Processes in Teicoplanin Biosynthesis. ACS Chem Biol 2016; 11:2254-64. [PMID: 27285718 DOI: 10.1021/acschembio.6b00018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Actinoplanes teichomyceticus produces teicoplanin (Tcp), a "last resort" lipoglycopeptide antibiotic used to treat severe multidrug resistant infections such as methicillin-resistant Staphylococcus aureus (MRSA). A number of studies have addressed various steps of Tcp biosynthesis using in vitro assays, although the exact sequence of Tcp peptide core tailoring reactions remained speculative. Here, we describe the generation and analysis of a set of A. teichomyceticus mutant strains that have been used to elucidate the sequence of reactions from the Tcp aglycone to mature Tcp. By combining these results with previously published data, we propose an updated order of post-assembly line tailoring processes in Tcp biosynthesis. We also demonstrate that the acyl-CoA-synthetase Tei13* and the type II thioesterase Tei30* are dispensable for Tcp production. Five Tcp derivatives featuring hitherto undescribed combinations of glycosylation and acylation patterns are described. The generation of strains that produce novel Tcp analogues now provides a platform for the production of additional Tcp-like molecules via combinatorial biosynthesis or chemical derivatization.
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Affiliation(s)
- Oleksandr Yushchuk
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Bohdan Ostash
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Thu H. Pham
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Andriy Luzhetskyy
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infectious Research (HZI), Saarbrucken, Germany
| | - Victor Fedorenko
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andrew W. Truman
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Liliya Horbal
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
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13
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Winn M, Fyans JK, Zhuo Y, Micklefield J. Recent advances in engineering nonribosomal peptide assembly lines. Nat Prod Rep 2016; 33:317-47. [PMID: 26699732 DOI: 10.1039/c5np00099h] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nonribosomal peptides are amongst the most widespread and structurally diverse secondary metabolites in nature with many possessing bioactivity that can be exploited for therapeutic applications. Due to the major challenges associated with total- and semi-synthesis, bioengineering approaches have been developed to increase yields and generate modified peptides with improved physicochemical properties or altered bioactivity. Here we review the major advances that have been made over the last decade in engineering the biosynthesis of nonribosomal peptides. Structural diversity has been introduced by the modification of enzymes required for the supply of precursors or by heterologous expression of tailoring enzymes. The modularity of nonribosomal peptide synthetase (NRPS) assembly lines further supports module or domain swapping methodologies to achieve changes in the amino acid sequence of nonribosomal peptides. We also review the new synthetic biology technologies promising to speed up the process, enabling the creation and optimisation of many more assembly lines for heterologous expression, offering new opportunities for engineering the biosynthesis of novel nonribosomal peptides.
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Affiliation(s)
- M Winn
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - J K Fyans
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Y Zhuo
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - J Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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14
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Salunke DM, Khan T, Gaur V, Tapryal S, Kaur K. Response to Comment on Three X-ray Crystal Structure Papers. THE JOURNAL OF IMMUNOLOGY 2016; 196:524-8. [PMID: 26747566 DOI: 10.4049/jimmunol.1501474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
| | - Tarique Khan
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Vineet Gaur
- International Institute of Molecular and Cell Biology; Warsaw 02-109, Poland
| | - Suman Tapryal
- Department of Biotechnology, Central University of Rajasthan, Bandarsindri-305817, India; and
| | - Kanwaljeet Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
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15
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Ariyasu S, Too PC, Mu J, Goh CC, Ding Y, Tnay YL, Yeow EKL, Yang L, Ng LG, Chiba S, Xing B. Glycopeptide antibiotic analogs for selective inactivation and two-photon imaging of vancomycin-resistant strains. Chem Commun (Camb) 2016; 52:4667-70. [DOI: 10.1039/c5cc10230h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Theranostic divalent vancomycin systems exhibit selective antibacterial activity against vancomycin-resistant strains and can be applied for two-photon fluorescence imaging.
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16
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Yoganathan S, Miller SJ. Structure diversification of vancomycin through peptide-catalyzed, site-selective lipidation: a catalysis-based approach to combat glycopeptide-resistant pathogens. J Med Chem 2015; 58:2367-77. [PMID: 25671771 DOI: 10.1021/jm501872s] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of antibiotic-resistant infections highlights the need for novel antibiotic leads, perhaps with a broader spectrum of activity. Herein, we disclose a semisynthetic, catalytic approach for structure diversification of vancomycin. We have identified three unique peptide catalysts that exhibit site-selectivity for the lipidation of the aliphatic hydroxyls on vancomycin, generating three new derivatives 9a, 9b, and 9c. Incorporation of lipid chains into the vancomycin scaffold provides promising improvement of its bioactivity against vancomycin-resistant enterococci (Van A and Van B phenotypes of VRE). The MICs for 9a, 9b, and 9c against MRSA and VRE (Van B phenotype) range from 0.12 to 0.25 μg/mL. We have also performed a structure-activity relationship (SAR) study to investigate the effect of lipid chain length at the newly accessible G4-OH derivatization site.
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Affiliation(s)
- Sabesan Yoganathan
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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