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Filipek J, Chalaskiewicz K, Kosmider A, Nielipinski M, Michalak A, Bednarkiewicz M, Goslawski-Zeligowski M, Prucnal F, Sekula B, Pietrzyk-Brzezinska AJ. Comprehensive structural overview of the C-terminal ligand-binding domains of the TetR family regulators. J Struct Biol 2024; 216:108071. [PMID: 38401830 DOI: 10.1016/j.jsb.2024.108071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
TetR family regulators (TFRs) represent a large group of one-component bacterial signal transduction systems which recognize environmental signals, like the presence of antibiotics or other bactericidal compounds, and trigger the cell response by regulating the expression of genes that secure bacterial survival in harsh environmental conditions. TFRs act as homodimers, each protomer is composed of a conserved DNA-binding N-terminal domain (NTD) and a variable ligand-binding C-terminal domain (CTD). Currently, there are about 500 structures of TFRs available in the Protein Data Bank and one-fourth of them represent the structures of TFR-ligand complexes. In this review, we summarized information on the ligands interacting with TFRs and based on structural data, we compared the CTDs of the TFR family members, as well as their ligand-binding cavities. Additionally, we divided the whole TFR family, including more than half of a million sequences, into subfamilies according to calculated multiple sequence alignment and phylogenetic tree. We also highlighted structural elements characteristic of some of the subfamilies. The presented comprehensive overview of the TFR CTDs provides good bases and future directions for further studies on TFRs that are not only important targets for battling multidrug resistance but also good candidates for many biotechnological approaches, like TFR-based biosensors.
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Affiliation(s)
- Jakub Filipek
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Katarzyna Chalaskiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Aleksandra Kosmider
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maciej Nielipinski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka Michalak
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maria Bednarkiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Mieszko Goslawski-Zeligowski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Filip Prucnal
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Bartosz Sekula
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland.
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Salgado H, Gama-Castro S, Lara P, Mejia-Almonte C, Alarcón-Carranza G, López-Almazo AG, Betancourt-Figueroa F, Peña-Loredo P, Alquicira-Hernández S, Ledezma-Tejeida D, Arizmendi-Zagal L, Mendez-Hernandez F, Diaz-Gomez AK, Ochoa-Praxedis E, Muñiz-Rascado LJ, García-Sotelo JS, Flores-Gallegos FA, Gómez L, Bonavides-Martínez C, del Moral-Chávez VM, Hernández-Alvarez AJ, Santos-Zavaleta A, Capella-Gutierrez S, Gelpi JL, Collado-Vides J. RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12. Nucleic Acids Res 2024; 52:D255-D264. [PMID: 37971353 PMCID: PMC10767902 DOI: 10.1093/nar/gkad1072] [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: 09/15/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.
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Affiliation(s)
- Heladia Salgado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Paloma Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Citlalli Mejia-Almonte
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Gabriel Alarcón-Carranza
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Andrés G López-Almazo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Felipe Betancourt-Figueroa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Pablo Peña-Loredo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | | | - Daniela Ledezma-Tejeida
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Lizeth Arizmendi-Zagal
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Francisco Mendez-Hernandez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Ana K Diaz-Gomez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Elizabeth Ochoa-Praxedis
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Luis J Muñiz-Rascado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Jair S García-Sotelo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Querétaro, Mexico
| | - Fanny A Flores-Gallegos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Laura Gómez
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan, 14610 Ciudad de México, Mexico
- Escuela de Medicina, Tecnológico de Monterrey, Campus Ciudad de México, CDMX 14380, Meéxico
| | - César Bonavides-Martínez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Víctor M del Moral-Chávez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | | | - Alberto Santos-Zavaleta
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, Morelos 62580, Meéxico
| | | | - Josep Lluis Gelpi
- Department of Biochemistry and Molecular Biomedicine. Univ. of Barcelona. Av. Diagonal 643, 08028, Barcelona, Spain
- Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra(UPF), Dr. Aiguader 88, Barcelona, 08003, Barcelona, Spain
| | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
- Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra(UPF), Dr. Aiguader 88, Barcelona, 08003, Barcelona, Spain
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall. Boston, MA 02215, USA
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The antidiabetic drug metformin aids bacteria in hijacking vitamin B12 from the environment through RcdA. Commun Biol 2023; 6:96. [PMID: 36693976 PMCID: PMC9873799 DOI: 10.1038/s42003-023-04475-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Years of use of the antidiabetic drug metformin has long been associated with the risk of vitamin B12 (B12) deficiency in type 2 diabetes (T2D) patients, although the underlying mechanisms are unclear. Accumulating evidence has shown that metformin may exert beneficial effects by altering the metabolism of the gut microbiota, but whether it induces human B12 deficiency via modulation of bacterial activity remains poorly understood. Here, we show that both metformin and the other biguanide drug phenformin markedly elevate the accumulation of B12 in E. coli. By functional and genomic analysis, we demonstrate that both biguanides can significantly increase the expression of B12 transporter genes, and depletions of vital ones, such as tonB, nearly completely abolish the drugs' effect on bacterial B12 accumulation. Via high-throughput screens in E. coli and C. elegans, we reveal that the TetR-type transcription factor RcdA is required for biguanide-mediated promotion of B12 accumulation and the expressions of B12 transporter genes in bacteria. Together, our study unveils that the antidiabetic drug metformin helps bacteria gather B12 from the environment by increasing the expressions of B12 transporter genes in an RcdA-dependent manner, which may theoretically reduce the B12 supply to T2D patients taking the drug over time.
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Qiao J, Liang Y, Wang Y. Trimethylamine N-Oxide Reduces the Susceptibility of Escherichia coli to Multiple Antibiotics. Front Microbiol 2022; 13:956673. [PMID: 35875516 PMCID: PMC9300990 DOI: 10.3389/fmicb.2022.956673] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Trimethylamine N-oxide (TMAO), an important intestinal flora-derived metabolite, plays a role in the development of cardiovascular disease and tumor immunity. Here, we determined the minimum inhibitory concentration (MIC) of antibiotics against Escherichia coli under gradient concentrations of TMAO and performed a bacterial killing analysis. Overall, TMAO (in the range of 10 ~ 100 mM) increased the MIC of quinolones, aminoglycosides, and β-lactams in a concentration-dependent manner, and increased the lethal dose of antibiotics against E. coli. It implies that TMAO is a potential risk for failure of anti-infective therapy, and presents a case for the relationship between intestinal flora-derived metabolites and antibiotic resistance. Further data demonstrated that the inhibition of antibiotic efficacy by TMAO is independent of the downstream metabolic processes of TMAO and the typical bacterial resistance mechanisms (mar motif and efflux pump). Interestingly, TMAO protects E. coli from high-protein denaturant (urea) stress and improves the viability of bacteria following treatment with two disinfectants (ethanol and hydrogen peroxide) that mediate protein denaturation by chemical action or oxidation. Since antibiotics can induce protein inactivation directly or indirectly, our work suggests that disruption of protein homeostasis may be a common pathway for different stress-mediated bacterial growth inhibition/cell death. In addition, we further discuss this possibility, which provides a different perspective to address the global public health problem of antibiotic resistance.
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Affiliation(s)
- Jiaxin Qiao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yan Liang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yao Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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