1
|
Wang L, Cao X, Pei H, Liu P, Song Y, Wu Y. Anti-Biofilm Activity of Chlorogenic Acid against Pseudomonas Using Quorum Sensing System. Foods 2023; 12:3601. [PMID: 37835254 PMCID: PMC10572673 DOI: 10.3390/foods12193601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Chlorogenic acid is a secondary metabolite produced by many traditional Chinese medicines. Its physiological activities (antibacterial, anti-inflammatory, antioxidant activities, etc.) have been well described. This study aimed to investigate the effects of chlorogenic acid on the biofilm of drinking water bacteria. The effects of chlorogenic acid on the metabolites of the biofilms were also evaluated. Chlorogenic acid was found to have an anti-biofilm effect against Pseudomonas, resulting in biofilm formation in a dose-dependent manner (0.53-25.4 mM CGA). Moreover, the biofilm structure was visibly attenuated. Furthermore, we identified and characterized 23 differential metabolites and associated two metabolic pathways involving beta-alanine metabolism and pyrimidine metabolism that were altered mostly during biofilm formation. A quantitative real-time PCR assay revealed that chlorogenic acid interfered with the signaling molecule synthesis and transcription regulators using the Las, Pqs and Rhl systems. These findings suggest that chlorogenic acid can be a quorum sensing (QS) inhibitor and inhibit biofilm formation. It may be a promising natural product for the prevention of contaminated drinking water.
Collapse
Affiliation(s)
- Lin Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (L.W.); (P.L.); (Y.S.); (Y.W.)
- School of Light Industry, Beijing Technology and Business University, Beijing 100037, China
| | - Xueli Cao
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (L.W.); (P.L.); (Y.S.); (Y.W.)
| | - Hairun Pei
- School of Light Industry, Beijing Technology and Business University, Beijing 100037, China
| | - Ping Liu
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (L.W.); (P.L.); (Y.S.); (Y.W.)
- School of Light Industry, Beijing Technology and Business University, Beijing 100037, China
| | - Ya Song
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (L.W.); (P.L.); (Y.S.); (Y.W.)
- School of Light Industry, Beijing Technology and Business University, Beijing 100037, China
| | - Yulun Wu
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; (L.W.); (P.L.); (Y.S.); (Y.W.)
- School of Light Industry, Beijing Technology and Business University, Beijing 100037, China
| |
Collapse
|
2
|
A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens. Biosci Rep 2020; 40:225330. [PMID: 32614053 PMCID: PMC7332683 DOI: 10.1042/bsr20201642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 11/21/2022] Open
Abstract
Dihydropyrimidine dehydrogenase (PydA) catalyzes the first step of the reductive pyrimidine degradation (Pyd) pathway in bacteria and eukaryotes, enabling pyrimidines to be utilized as substrates for growth. PydA homologs studied to date catalyze the reduction of uracil to dihydrouracil, coupled to the oxidation of NAD(P)H. Uracil reduction occurs at a flavin mononucleotide (FMN) site, and NAD(P)H oxidation occurs at a flavin adenine dinucleotide (FAD) site, with two ferredoxin domains thought to mediate inter-site electron transfer. Here, we report the biochemical characterization of a Clostridial PydA homolog (PydAc) from a Pyd gene cluster in the strict anaerobic bacterium Clostridium chromiireducens. PydAc lacks the FAD domain, and instead is able to catalyze uracil reduction using reduced methyl viologen or reduced ferredoxin as the electron source. Homologs of PydAc are present in Pyd gene clusters in many strict anaerobic bacteria, which use reduced ferredoxin as an intermediate in their energy metabolism.
Collapse
|
3
|
A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium. Appl Environ Microbiol 2020; 86:AEM.02837-19. [PMID: 31953335 DOI: 10.1128/aem.02837-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/10/2020] [Indexed: 11/20/2022] Open
Abstract
Bacteria utilize diverse biochemical pathways for the degradation of the pyrimidine ring. The function of the pathways studied to date has been the release of nitrogen for assimilation. The most widespread of these pathways is the reductive pyrimidine catabolic pathway, which converts uracil into ammonia, carbon dioxide, and β-alanine. Here, we report the characterization of a β-alanine:pyruvate aminotransferase (PydD2) and an NAD+-dependent malonic semialdehyde dehydrogenase (MSDH) from a reductive pyrimidine catabolism gene cluster in Bacillus megaterium Together, these enzymes convert β-alanine into acetyl coenzyme A (acetyl-CoA), a key intermediate in carbon and energy metabolism. We demonstrate the growth of B. megaterium in defined medium with uracil as its sole carbon and energy source. Homologs of PydD2 and MSDH are found in association with reductive pyrimidine pathway genes in many Gram-positive bacteria in the order Bacillales Our study provides a basis for further investigations of the utilization of pyrimidines as a carbon and energy source by bacteria.IMPORTANCE Pyrimidine has wide occurrence in natural environments, where bacteria use it as a nitrogen and carbon source for growth. Detailed biochemical pathways have been investigated with focus mainly on nitrogen assimilation in the past decades. Here, we report the discovery and characterization of two important enzymes, PydD2 and MSDH, which constitute an extension for the reductive pyrimidine catabolic pathway. These two enzymes, prevalent in Bacillales based on our bioinformatics studies, allow stepwise conversion of β-alanine, a previous "end product" of the reductive pyrimidine degradation pathway, to acetyl-CoA as carbon and energy source.
Collapse
|
4
|
Panda AK, Bisht SS, DeMondal S, Senthil Kumar N, Gurusubramanian G, Panigrahi AK. Brevibacillus as a biological tool: a short review. Antonie van Leeuwenhoek 2014; 105:623-39. [DOI: 10.1007/s10482-013-0099-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/11/2013] [Indexed: 01/12/2023]
|
5
|
Nandanwar HS, Prajapati R, Hoondal GS. (D)-p-Hydroxyphenylglycine production by thermostable D-hydantoinase fromBrevibacillus parabrevis-PHG1. BIOCATAL BIOTRANSFOR 2013. [DOI: 10.3109/10242422.2012.755962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
6
|
Simultaneous purification and immobilization of d-hydantoinase on the immobilized metal affinity membrane via coordination bonds. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2011.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
7
|
Ko YM, Chen CI, Chang HC, Chen HM, Shieh CJ, Syu YJ, Liu YC. Exploring the complex effects of metal ions on d-hydantoinase purification with an immobilized metal affinity membrane. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2011.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Zrenner R, Riegler H, Marquard CR, Lange PR, Geserick C, Bartosz CE, Chen CT, Slocum RD. A functional analysis of the pyrimidine catabolic pathway in Arabidopsis. THE NEW PHYTOLOGIST 2009; 183:117-132. [PMID: 19413687 PMCID: PMC2713857 DOI: 10.1111/j.1469-8137.2009.02843.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/19/2009] [Indexed: 05/04/2023]
Abstract
* Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to beta-alanine, CO(2) and NH(3) through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and beta-ureidopropionase (EC 3.5.1.6, PYD3). * A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-(14)C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source. * PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-(14)C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant. * The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation.
Collapse
Affiliation(s)
- Rita Zrenner
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
- Leibniz-Institute of Vegetable and Ornamental Crops14979 Großbeeren, Germany
| | - Heike Riegler
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Cathleen R Marquard
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Peter R Lange
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Claudia Geserick
- Max Planck Institute of Molecular Plant Physiology14476 Potsdam OT Golm, Germany
| | - Caren E Bartosz
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
| | - Celine T Chen
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
| | - Robert D Slocum
- Department of Biological Sciences, Goucher CollegeBaltimore, MD 21204-2794, USA
| |
Collapse
|
9
|
Lo CK, Kao CH, Wang WC, Wu HM, Hsu WH, Lin LL, Hu HY. Engineering of the critical residues at the stereochemistry-gate loops of Brevibacillus agri dihydropyrimidinase for the production of l-homophenylalanine. Process Biochem 2009. [DOI: 10.1016/j.procbio.2008.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
10
|
Dürr R, Neumann A, Vielhauer O, Altenbuchner J, Burton S, Cowan D, Syldatk C. Genes responsible for hydantoin degradation of a halophilic Ochrobactrum sp. G21 and Delftia sp. I24 — New insight into relation of d-hydantoinases and dihydropyrimidinases. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2007.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
11
|
Piskur J, Schnackerz KD, Andersen G, Björnberg O. Comparative genomics reveals novel biochemical pathways. Trends Genet 2007; 23:369-72. [PMID: 17555842 DOI: 10.1016/j.tig.2007.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 04/17/2007] [Accepted: 05/23/2007] [Indexed: 10/23/2022]
Abstract
How well do we understand which enzymes are involved in the primary metabolism of the cell? A recent study using comparative genomics and postgenomics approaches revealed a novel pathway in the most studied organism, Escherichia coli. The analysis of a new operon consisting of seven previously uncharacterized genes thought to be involved in the degradation of nucleic acid precursors shows the impact of comparative genomics on the discovery of novel pathways and enzymes.
Collapse
Affiliation(s)
- Jure Piskur
- Department of Cell and Organism Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.
| | | | | | | |
Collapse
|
12
|
Effect of number of poly(His) tags on the adsorption of engineered proteins on immobilized metal affinity chromatography adsorbents. Process Biochem 2006. [DOI: 10.1016/j.procbio.2006.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
13
|
Affiliation(s)
- Andrei Osterman
- Burnham Institute for Medical Research, La Jolla, CA 92037, USA.
| |
Collapse
|
14
|
Lin LL, Hsu WH, Hsu WY, Kan SC, Hu HY. Phylogenetic Analysis and Biochemical Characterization of a Thermostable Dihydropyrimidinase from Alkaliphilic Bacillus sp. TS-23. Antonie van Leeuwenhoek 2005; 88:189-97. [PMID: 16284925 DOI: 10.1007/s10482-005-5270-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 04/11/2005] [Indexed: 10/25/2022]
Abstract
Two degenerate primers established from the alignment of highly conserved amino acid sequences of bacterial dihydropyrimidinases (DHPs) were used to amplify a 330-bp gene fragment from the genomic DNA of Bacillus sp. TS-23 and the amplified DNA was successfully used as a probe to clone a dhp gene from the strain. The open reading frame of the gene consisted of 1422 bp and was deduced to contain 472 amino acids with a molecular mass of 52 kDa. The deduced amino acid sequence exhibited greater than 45% identity with that of prokaryotic D-hydantoinases and eukaryotic DHPs. Phylogenetic analysis showed that Bacillus sp. TS-23 DHP is grouped together with Bacillus stearothermophilus D-hydantoinase and related to dihydroorotases and allantoinases from various organisms. His6-tagged DHP was over-expressed in Escherichia coli and purified by immobilized metal affinity chromatography to a specific activity of 3.46 U mg(-1) protein. The optimal pH and temperature for the purified enzyme were 8.0 and 60 degrees C, respectively. The half-life of His6-tagged DHP was 25 days at 50 degrees C. The enzyme activity was stimulated by Co2+ and Mn2+ ions. His6-tagged DHP was most active toward dihydrouracil followed by hydantoin derivatives. The catalytic efficiencies (kcat/Km) of the enzyme for dihydrouracil and hydantoin were 2.58 and 0.61 s(-1) mM(-1), respectively.
Collapse
Affiliation(s)
- Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, Chiayi 60083, Taiwan
| | | | | | | | | |
Collapse
|