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Jiang Y, Wang K, Xu L, Xu L, Xu Q, Mu Y, Hong Q, He J, Jiang J, Qiu J. DipR, a GntR/FadR-family transcriptional repressor: regulatory mechanism and widespread distribution of the dip cluster for dipicolinic acid catabolism in bacteria. Nucleic Acids Res 2024:gkae728. [PMID: 39180394 DOI: 10.1093/nar/gkae728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
Dipicolinic acid is an essential component of bacterial spores for stress resistance, which is released into the environment after spore germination. In a previous study, a dip gene cluster was found to be responsible for the catabolism of dipicolinic acid in Alcaligenes faecalis JQ135. However, the transcriptional regulatory mechanism remains unclear. The present study characterized the new GntR/FadR family transcriptional factor DipR, showing that the dip cluster is transcribed as the six transcriptional units, dipR, dipA, dipBC, dipDEFG, dipH and dipJKLM. The purified DipR protein has six binding sites sharing the 6-bp conserved motif sequence 5'-GWATAC-3'. Site-directed mutations indicated that these motif sequences are essential for DipR binding. Moreover, the four key amino acid residues R63, R67, H196 and H218 of DipR, examined by site-directed mutagenesis, played crucial roles in DipR regulation. Bioinformatics analysis showed that dip clusters including dipR genes are widely distributed in bacteria, are taxon-related, and co-evolved with their hosts. This paper provides new insights into the transcriptional regulatory mechanism of dipicolinic acid degradation by DipR in bacteria.
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Affiliation(s)
- Yinhu Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Kexin Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lu Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lanyi Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qimiao Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Mu
- Taizhou Center for Disease Prevention and Control, Taizhou 225300, China
| | - Qing Hong
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian He
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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2
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Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024; 53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.
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Affiliation(s)
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
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3
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Wang H, Zhang M, Wang E, Xiao R, Zhang S, Guo M. Agrobacterium fabrum gene atu1420 regulates the pathogenicity by affecting the degradation of growth- and virulence-associated phenols. Res Microbiol 2023; 174:104011. [PMID: 36455782 DOI: 10.1016/j.resmic.2022.104011] [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: 08/20/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Agrobacterium fabrum is a phytopathogen that causes the crown gall disease. Some plant-derived molecules, e.g. phenols, directly affect A. fabrum-plant interactions. Here, we characterize a phenolic catabolism-related gene, atu1420, that affects the pathogenicity of A. fabrum. Atu1420 is predicted to be an O-demethylase with high structural homology to Sphingomonas paucimobilis LigM. The HPLC-UV analysis showed that atu1420 affected the degradation of acetosyringone (AS). The deletion of atu1420 gene significantly enhanced the AS-induced virulence (vir) gene expression. atu1420 was shown to relieve the inhibitory effect of vanillic acid on the AS-induced vir gene expression and the growth of A. fabrum. The expression of atu1420 and the degradation of AS in A. fabrum C58 was up-regulated by the addition of indole acetic acid (IAA). The inhibitory effect of IAA on the AS-induced vir gene expression was partially relieved by the deletion of atu1420 gene, indicating that accelerating the degradation of AS is one of the ways that IAA inhibits vir genes induction. Furthermore, atu1420 mutant produced more pronounced tumors on kalanchoe leaves than the wild-type strain. These findings reveal the role of atu1420 in A. fabrum-host interactions and will broaden our understanding of the regulatory network of the interactions.
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Affiliation(s)
- Hao Wang
- Department of Biotechnology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
| | - Mengqi Zhang
- Department of Biotechnology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
| | - Erya Wang
- Department of Biotechnology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
| | - Ruoxuan Xiao
- Department of Biotechnology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
| | - Shuhang Zhang
- Department of Biotechnology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
| | - Minliang Guo
- Department of Biotechnology, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
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4
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Xu X, Yan Y, Huang J, Zhang Z, Wang Z, Wu M, Liang H. Regulation of uric acid and glyoxylate metabolism by UgmR protein in Pseudomonas aeruginosa. Environ Microbiol 2022; 24:3242-3255. [PMID: 35702827 DOI: 10.1111/1462-2920.16088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa has evolved several systems to adapt to complex environments. The GntR family proteins play important roles in the regulation of metabolic processes and bacterial pathogenesis. In this study, we uncovered that the gene clusters of PA1513-PA1518 and PA1498-PA1502 in P. aeruginosa are required for uric acid and glyoxylate metabolism, respectively. We also identified a GntR family regulator UgmR that is involved in regulation of uric acid and glyoxylate metabolism. Promoter activity measurement and biochemical assays revealed that the UgmR directly represses the transcriptional activity of PA1513-PA1518 and PA1498-PA1502, and this inhibition was relieved by the addition of uric acid. Importantly, further experiments showed that UgmR also participates in the glyoxylate shunt. Collectively, these findings contribute to a better understanding of the UgmR factor involved in uric acid and glyoxylate metabolism, which provide insights into the complex metabolic pathways in P. aeruginosa. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xuejie Xu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Yunfang Yan
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Jiadai Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, SAR, China
| | - Zihao Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Zhihan Wang
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, ShaanXi, China.,College of Medicine, Southern University of Science and Technology, Shenzhen, China
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5
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Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer by native mass spectrometry. J Mol Biol 2022; 434:167480. [PMID: 35176290 PMCID: PMC8977229 DOI: 10.1016/j.jmb.2022.167480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022]
Abstract
FraR, a transcriptional repressor, was postulated to regulate the metabolism of the Amadori compound fructose-asparagine (F-Asn) in the foodborne pathogen Salmonella enterica. Here, the DNA- and inducer-binding affinities and stoichiometries of FraR were determined and cross-validated by electrophoretic mobility-shift assays (EMSAs) and online buffer exchange coupled to native mass spectrometry (OBE-nMS). We demonstrate the utility of OBE-nMS to characterize protein and protein-DNA complexes that are not amenable to offline exchange into volatile buffers. OBE-nMS complemented EMSAs by revealing that FraR binds to the operator DNA as a dimer and by establishing 6-phosphofructose-aspartate as the inducer that weakens DNA binding by FraR. These results provide insights into how FraR regulates the expression of F-Asn-catabolizing enzymes and add to our understanding of the intricate bacterial circuitry that dictates utilization of diverse nutrients.
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6
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Hermann L, Dempwolff F, Steinchen W, Freibert SA, Smits SHJ, Seubert A, Bremer E. The MocR/GabR Ectoine and Hydroxyectoine Catabolism Regulator EnuR: Inducer and DNA Binding. Front Microbiol 2022; 12:764731. [PMID: 35003002 PMCID: PMC8739950 DOI: 10.3389/fmicb.2021.764731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/01/2021] [Indexed: 11/26/2022] Open
Abstract
The compatible solutes ectoine and 5-hydroxyectoine are widely synthesized by bacteria as osmostress protectants. These nitrogen-rich tetrahydropyrimidines can also be exploited as nutrients by microorganisms. Many ectoine/5-hydroxyectoine catabolic gene clusters are associated with a regulatory gene (enuR: ectoine nutrient utilization regulator) encoding a repressor protein belonging to the MocR/GabR sub-family of GntR-type transcription factors. Focusing on EnuR from the marine bacterium Ruegeria pomeroyi, we show that the dimerization of EnuR is mediated by its aminotransferase domain. This domain can fold independently from its amino-terminal DNA reading head and can incorporate pyridoxal-5′-phosphate (PLP) as cofactor. The covalent attachment of PLP to residue Lys302 of EnuR was proven by mass-spectrometry. PLP interacts with system-specific, ectoine and 5-hydroxyectoine-derived inducers: alpha-acetyldiaminobutyric acid (alpha-ADABA), and hydroxy-alpha-acetyldiaminobutyric acid (hydroxy-alpha-ADABA), respectively. These inducers are generated in cells actively growing with ectoines as sole carbon and nitrogen sources, by the EutD hydrolase and targeted metabolic analysis allowed their detection. EnuR binds these effector molecules with affinities in the low micro-molar range. Studies addressing the evolutionary conservation of EnuR, modelling of the EnuR structure, and docking experiments with the inducers provide an initial view into the cofactor and effector binding cavity. In this cavity, the two high-affinity inducers for EnuR, alpha-ADABA and hydroxy-alpha-ADABA, are positioned such that their respective primary nitrogen group can chemically interact with PLP. Purified EnuR bound with micro-molar affinity to a 48 base pair DNA fragment containing the sigma-70 type substrate-inducible promoter for the ectoine/5-hydroxyectoine importer and catabolic gene cluster. Consistent with the function of EnuR as a repressor, the core elements of the promoter overlap with two predicted EnuR operators. Our data lend themselves to a straightforward regulatory model for the initial encounter of EnuR-possessing ectoine/5-hydroxyectoine consumers with environmental ectoines and for the situation when the external supply of these compounds has been exhausted by catabolism.
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Affiliation(s)
- Lucas Hermann
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany.,Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Felix Dempwolff
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Wieland Steinchen
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Sven-Andreas Freibert
- Department of Medicine, Institute for Cytobiology and Cytopathology, and SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University, Düsseldorf, Germany.,Center for Structural Studies (CSS), Faculty of Biochemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Andreas Seubert
- Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Erhard Bremer
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany.,SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
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Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G. BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Res 2021; 49:10166-10177. [PMID: 34432045 PMCID: PMC8517857 DOI: 10.1093/nar/gkab736] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.
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Affiliation(s)
- Adrian M Bandera
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Joseph Bartho
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Katja Lammens
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - David Jan Drexler
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Jasmin Kleinschwärzer
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Gregor Witte
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
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