1
|
Hernández-Rocamora VM, Molina R, Alba A, Carrasco-López C, Rojas-Altuve A, Panjikar S, Medina A, Usón I, Alfonso C, Galán B, Rivas G, Hermoso JA, Sanz JM. Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins. Int J Biol Macromol 2024; 254:127935. [PMID: 37949283 DOI: 10.1016/j.ijbiomac.2023.127935] [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: 07/20/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
PaaX is a transcriptional repressor of the phenylacetic acid (PAA) catabolic pathway, a central route for bacterial aerobic degradation of aromatic compounds. Induction of the route is achieved through the release of PaaX from its promoter sequences by the first compound of the pathway, phenylacetyl-coenzyme A (PA-CoA). We report the crystal structure of PaaX from Escherichia coli W. PaaX displays a novel type of fold for transcription regulators, showing a dimeric conformation where the monomers present a three-domain structure: an N-terminal winged helix-turn-helix domain, a dimerization domain similar to the Cas2 protein and a C-terminal domain without structural homologs. The domains are separated by a crevice amenable to harbour a PA-CoA molecule. The biophysical characterization of the protein in solution confirmed several hints predicted from the structure, i.e. its dimeric conformation, a modest importance of cysteines and a high dependence of solubility and thermostability on ionic strength. At a moderately acidic pH, the protein formed a stable folding intermediate with remaining α-helical structure, a disrupted tertiary structure and exposed hydrophobic patches. Our results provide valuable information to understand the stability and mechanism of PaaX and pave the way for further analysis of other regulators with similar structural configurations.
Collapse
Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Av. Universidad, s/n, E-03202 Elche, Alicante, Spain; Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alejandra Alba
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alzoray Rojas-Altuve
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain; ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
2
|
Ameer NAA, Dhahi MAR. Alterations in gene expression of recA and umuDC in antibiotic-resistant Acinetobacter baumannii. J Med Life 2023; 16:531-539. [PMID: 37305826 PMCID: PMC10251391 DOI: 10.25122/jml-2022-0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/01/2023] [Indexed: 06/13/2023] Open
Abstract
Acinetobacter baumannii is a critical pathogen with an efficient SOS (Save Our Ship) system that plays a significant role in antibiotic resistance. This prospective descriptive study aimed to investigate the association between expression levels of recA and umuDC genes, which are critical in SOS pathways, and antibiotic resistance in A. baumannii. We analyzed 78 clinical isolates and 31 ecological isolates using the Vitek-2 system for bacterial identification and antibiotic susceptibility testing and confirmed molecular identification of A. baumannii by conventional PCR of blaOXA-51 and blaOXA-23. Quantitative real-time polymerase chain reaction was used to determine gene expression levels of recA and umuDC. The results showed that in 25 clinical strains, 14/25 strains showed upregulation of recA, 7/25 strains exhibited upregulation of both umuDC and recA, and 1/25 strains showed upregulation of umuDC. Of these, 16/25 clinical strains were extensively resistant to antibiotics, except for colistin, and showed upregulation of recA and/or umuDC gene expression levels. In 6 ecological strains, recA showed upregulation in 3/6 strains, while both recA and umuDC were upregulated in 1/6 strain. In conclusion, high expression levels of recA and/or umuDC genes in A. baumannii complex and A. baumannii strains may contribute to increasing resistance to a wide range of antibiotics and may result in the initiation of an extensively drug-resistant (XDR) phenotype.
Collapse
|
3
|
A Bibliometric Analysis of Research on Bacterial Persisters. BIOMED RESEARCH INTERNATIONAL 2023; 2023:4302914. [PMID: 36644164 PMCID: PMC9839416 DOI: 10.1155/2023/4302914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/30/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Background In the past two decades, the surge of research on bacterial persisters has been inspired as increasingly concerning about the frequent failure of antibiotics treatment. This study was aimed at presenting a bibliometric and visualized analysis of relative publications on bacterial persisters, which offered insights into the development and research trends of this field. Methods The Web of Science Core Collection and Ovid MEDLINE databases were utilized to retrieve relevant publications on bacterial persisters from 2001 to 2021. After manual selection, data including titles, authors, journals, author keywords, addresses, the number of citations, and publication years were subsequently extracted. The data analysis and visual mapping were conducted with Excel, SPSS, R studio, and VOSviewer. Results In this study, 1,903 relevant publications on bacterial persisters were included. During 2001-2021, there was an exponential growth in the quantity of publications. It was found that these studies were conducted by 7,182 authors from 74 different countries. The USA led the scientific production with the highest total number of publications (859) and citation frequency (52,022). The Antimicrobial Agents and Chemotherapy was the most influential journal with 113 relevant publications. The cooccurrence analysis revealed that studies on bacterial persisters focused on four aspects: "the role of persisters in biofilms," "clinical persistent infection," "anti-persister treatment," and "mechanism of persister formation." Conclusion In the past two decades, the global field of bacterial persisters has significantly increased. The USA was the leading country in this field. Mechanistic studies continued to be the future hotspots, which may be helpful to adopt new strategies against persisters and solve the problem of chronic infection in the clinic.
Collapse
|
4
|
The DdrR Coregulator of the Acinetobacter baumannii Mutagenic DNA Damage Response Potentiates UmuDAb Repression of Error-Prone Polymerases. J Bacteriol 2022; 204:e0016522. [PMID: 36194009 PMCID: PMC9664961 DOI: 10.1128/jb.00165-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii
is a nosocomial pathogen that acquires antibiotic resistance genes through conjugative transfer and carries out a robust mutagenic DNA damage response. After exposure to conditions typically encountered in health care settings, such as antibiotics, UV light, and desiccation, this species induces error-prone UmuD′
2
C polymerases.
Collapse
|
5
|
Jiao M, He W, Ouyang Z, Shi Q, Wen Y. Progress in structural and functional study of the bacterial phenylacetic acid catabolic pathway, its role in pathogenicity and antibiotic resistance. Front Microbiol 2022; 13:964019. [PMID: 36160191 PMCID: PMC9493321 DOI: 10.3389/fmicb.2022.964019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Phenylacetic acid (PAA) is a central intermediate metabolite involved in bacterial degradation of aromatic components. The bacterial PAA pathway mainly contains 12 enzymes and a transcriptional regulator, which are involved in biofilm formation and antimicrobial activity. They are present in approximately 16% of the sequenced bacterial genome. In this review, we have summarized the PAA distribution in microbes, recent structural and functional study progress of the enzyme families of the bacterial PAA pathway, and their role in bacterial pathogenicity and antibiotic resistance. The enzymes of the bacterial PAA pathway have shown potential as an antimicrobial drug target for biotechnological applications in metabolic engineering.
Collapse
Affiliation(s)
- Min Jiao
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Wenbo He
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Zhenlin Ouyang
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Qindong Shi
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Yurong Wen
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Yurong Wen,
| |
Collapse
|
6
|
Tobramycin Stress Induced Differential Gene Expression in Acinetobacter baumannii. Curr Microbiol 2022; 79:88. [PMID: 35129693 DOI: 10.1007/s00284-022-02788-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/24/2022] [Indexed: 11/03/2022]
Abstract
Acinetobacter baumannii is a multidrug-resistant bacteria responsible for nosocomial infections with significant fatality rates globally. Therapeutic failure and relapse of infection has been associated with persister cells formation which can also lead to resistance in A. baumannii. In the present study, we observed that A. baumannii ATCC 17978 in exponential phase survived lethal concentrations of amikacin, rifampicin and ciprofloxacin by generating persister cells but was unable to survive tobramycin treatment. The transcriptome of A. baumannii ATCC 17978 was analyzed following exposure to a high concentration of tobramycin (10 × MIC) for a short period of time to study the possible mechanisms responsible for lethality. Tobramycin reduced the expression of genes involved in energy production (nuoH, nuoN, nuoM, cydA, sucC), oxidative stress protection (tauD, cysD), and nutrition uptake (ompW) significantly. In addition, hemerythrin (non-heme di-iron oxygen-binding protein) was found to be the most downregulated gene in response to tobramycin which needs to be further studied for its role in susceptibility to antibiotics. Tobramycin upregulated the expression of genes that are mainly involved in stress response (leucine catabolism, DNA repair and HicAB toxin-antitoxin system). The differentially expressed genes highlighted in the study provided insight into the probable molecular mechanism of tobramycin-induced cell death and revealed some novel targets that can be explored further for their potential to control A. baumannii.
Collapse
|