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Jeong Y, Moon S, Shin JH. In vitro synthesis and biochemical characterization of acyl-homoserine lactone synthase and its deletion mutant. PLoS One 2024; 19:e0304331. [PMID: 38820426 PMCID: PMC11142500 DOI: 10.1371/journal.pone.0304331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 05/09/2024] [Indexed: 06/02/2024] Open
Abstract
Quorum sensing can induce density-dependent gene expressions that cause various problems. For quorum-sensing inhibition, fundamental solutions such as gene manipulation are required, and acyl-homoserine lactone synthase (AHL synthase), which synthesizes the universal quorum-sensing signal of gram-negative bacteria, can be used as a target. In this study, researchers synthesized His-tagged AHL synthase and its deletion mutant that lacks the active site and compared their biochemical characteristics. His-YpeI, the 6x His-tagged AHL synthase of Serratia fonticola, and His-ΔYpeI, its deletion mutant, were designed, and their property conservation were examined using in silico projection tools. For in vitro synthesis of enzymes, the His-YpeI CFPS template was synthesized by in vitro gene synthesis, and the His-ΔYpeI CFPS template was obtained by deletion PCR. CFPS was performed and the products were purified with the 6x His-tag. The enzymes' properties were compared using an enzymatic assay. The bioinformatic analysis confirmed the conservation of biochemical properties between 6x His-tagged and untagged enzymes, including helix-turn-helix interactions, hydropathy profiles, and tertiary structure between His-YpeI and YpeI and between His-ΔYpeI and ΔYpeI. His-YpeI and His-ΔYpeI synthesized by CFPS were found to have the expected molecular weights and demonstrated distinct differences in enzyme activity. The analyzed enzymatic constants supported a significant decrease in substrate affinity and reaction rate as a result of YpeI's enzyme active site deletion. This result showed that CFPS could be used for in vitro protein synthesis, and quorum sensing could be inhibited at the enzymatic level due to the enzyme active site's deletion mutation.
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Affiliation(s)
- Yechan Jeong
- Gyeonggi Science High School for the Gifted, Suwon, Gyeonggi, Republic of Korea
| | - Sunwoo Moon
- Gyeonggi Science High School for the Gifted, Suwon, Gyeonggi, Republic of Korea
| | - Jae-hwa Shin
- Gyeonggi Science High School for the Gifted, Suwon, Gyeonggi, Republic of Korea
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Shin D, Gorgulla C, Boursier ME, Rexrode N, Brown EC, Arthanari H, Blackwell HE, Nagarajan R. N-Acyl Homoserine Lactone Analog Modulators of the Pseudomonas aeruginosa Rhll Quorum Sensing Signal Synthase. ACS Chem Biol 2019; 14:2305-2314. [PMID: 31545595 DOI: 10.1021/acschembio.9b00671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Virulence in the Gram-negative pathogen Pseudomonas aeruginosa relies in part on the efficient functioning of two LuxI/R dependent quorum sensing (QS) cascades, namely, the LasI/R and RhlI/R systems that generate and respond to N-(3-oxo)-dodecanoyl-l-homoserine lactone and N-butyryl-l-homoserine lactone, respectively. The two acyl homoserine lactone (AHL) synthases, LasI and RhlI, use 3-oxododecanoyl-ACP and butyryl-ACP, respectively, as the acyl-substrates to generate the corresponding autoinducer signals for the bacterium. Although AHL synthases represent excellent targets for developing QS modulators in P. aeruginosa, and in other related bacteria, the identification of potent and signal synthase specific inhibitors has represented a significant technical challenge. In the current study, we sought to test the utility of AHL analogs as potential modulators of an AHL synthase and selected RhlI in P. aeruginosa as an initial target. We systematically varied the chemical functionalities of the AHL headgroup, acyl chain tail, and head-to-tail linkage to construct a small library of signal analogs and evaluated them for RhlI modulatory activity. Although the native N-butyryl-l-homoserine lactone did not inhibit RhlI, we discovered that several of our long-chain, unsubstituted acyl-d-homoserine lactones and acyl-d-homocysteine thiolactones inhibited while a few of the 3-oxoacyl-chain counterparts activated the enzyme. Additional mechanistic investigations with acyl-substrate analogs and docking experiments with AHL analogs revealed two distinct inhibitor and activator binding pockets in the enzyme. This study provides the first evidence of the yet untapped potential of AHL analogs as signal synthase modulators of QS pathways.
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Affiliation(s)
- Daniel Shin
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, Massachusetts 02115, United States
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Michelle E. Boursier
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Neilson Rexrode
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Eric C. Brown
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
| | - Rajesh Nagarajan
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
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Nhu Lam M, Dudekula D, Durham B, Collingwood N, Brown EC, Nagarajan R. Insights into β-ketoacyl-chain recognition for β-ketoacyl-ACP utilizing AHL synthases. Chem Commun (Camb) 2018; 54:8838-8841. [PMID: 30027952 DOI: 10.1039/c8cc04532a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Beta-ketoacyl-ACP utilizing enzymes in fatty acid, polyketide and acyl-homoserine lactone biosynthetic pathways are important targets for developing antimicrobial, anticancer and antiparasitic compounds. Published reports on successful isolation of beta-ketoacyl-ACPs in a laboratory remain scarce to date and thus most beta-ketoacyl-ACP utilizing enzymes are routinely characterized using small molecule substrates in lieu of the bonafide 3-oxoacyl-ACPs. We report the systematic investigation into the electronic, geometric and spatial aspects of beta-ketoacyl-chain recognition to develop 3-oxoacyl-ACP substrate mimics for two beta-ketoacyl-ACP utilizing quorum signal synthases.
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Affiliation(s)
- Mila Nhu Lam
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr, Boise, ID 83725, USA.
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Shin D, Nagarajan R. Enzymatic Assays to Investigate Acyl-Homoserine Lactone Autoinducer Synthases. Methods Mol Biol 2018; 1673:161-176. [PMID: 29130172 PMCID: PMC5766357 DOI: 10.1007/978-1-4939-7309-5_13] [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] [Indexed: 06/07/2023]
Abstract
Bacteria use chemical molecules called autoinducers as votes to poll their numerical strength in a colony. This polling mechanism, commonly referred to as quorum sensing, enables bacteria to build a social network and provide a collective response for fighting off common threats. In Gram-negative bacteria, AHL synthases synthesize acyl-homoserine lactone (AHL) autoinducers to turn on the expression of several virulent genes including biofilm formation, protease secretion, and toxin production. Therefore, inhibiting AHL signal synthase would limit quorum sensing and virulence. In this chapter, we describe four enzymatic methods that could be adopted to investigate a broad array of AHL synthases. The enzymatic assays described here should accelerate our mechanistic understanding of quorum-sensing signal synthesis that could pave the way for discovery of potent antivirulence compounds.
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Affiliation(s)
- Daniel Shin
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Rajesh Nagarajan
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA.
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Welsh MA, Blackwell HE. Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiol Rev 2016; 40:774-94. [PMID: 27268906 DOI: 10.1093/femsre/fuw009] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 01/20/2023] Open
Abstract
Bacteria can utilize chemical signals to coordinate the expression of group-beneficial behaviors in a method of cell-cell communication called quorum sensing (QS). The discovery that QS controls the production of virulence factors and biofilm formation in many common pathogens has driven an explosion of research aimed at both deepening our fundamental understanding of these regulatory networks and developing chemical agents that can attenuate QS signaling. The inherently chemical nature of QS makes studying these pathways with small molecule tools a complementary approach to traditional microbiology techniques. Indeed, chemical tools are beginning to yield new insights into QS regulation and provide novel strategies to inhibit QS. Here, we review the most recent advances in the development of chemical probes of QS systems in Gram-negative bacteria, with an emphasis on the opportunistic pathogen Pseudomonas aeruginosa We first describe reports of novel small molecule modulators of QS receptors and QS signal synthases. Next, in several case studies, we showcase how chemical tools have been deployed to reveal new knowledge of QS biology and outline lessons for how researchers might best target QS to combat bacterial virulence. To close, we detail the outstanding challenges in the field and suggest strategies to overcome these issues.
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Affiliation(s)
- Michael A Welsh
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
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