1
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Cervoni M, Sposato D, Ferri G, Bähre H, Leoni L, Rampioni G, Visca P, Recchiuti A, Imperi F. The diadenosine tetraphosphate hydrolase ApaH contributes to Pseudomonas aeruginosa pathogenicity. PLoS Pathog 2024; 20:e1012486. [PMID: 39159286 DOI: 10.1371/journal.ppat.1012486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
The opportunistic bacterial pathogen Pseudomonas aeruginosa causes a wide range of infections that are difficult to treat, largely because of the spread of antibiotic-resistant isolates. Antivirulence therapy, í.e. the use of drugs that inhibit the expression or activity of virulence factors, is currently considered an attractive strategy to reduce P. aeruginosa pathogenicity and complement antibiotic treatments. Because of the multifactorial nature of P. aeruginosa virulence and the broad arsenal of virulence factors this bacterium can produce, the regulatory networks that control the expression of multiple virulence traits have been extensively explored as potential targets for antivirulence drug development. The intracellular signaling molecule diadenosine tetraphosphate (Ap4A) has been reported to control stress resistance and virulence-related traits in some bacteria, but its role has not been investigated in P. aeruginosa so far. To fill this gap, we generated a mutant of the reference strain P. aeruginosa PAO1 that lacks the Ap4A-hydrolysing enzyme ApaH and, consequently, accumulates high intracellular levels of Ap4A. Phenotypic and transcriptomic analyses revealed that the lack of ApaH causes a drastic reduction in the expression of several virulence factors, including extracellular proteases, elastases, siderophores, and quorum sensing signal molecules. Accordingly, infection assays in plant and animal models demonstrated that ApaH-deficient cells are significantly impaired in infectivity and persistence in different hosts, including mice. Finally, deletion of apaH in P. aeruginosa clinical isolates demonstrated that the positive effect of ApaH on the production of virulence-related traits and on infectivity is conserved in P. aeruginosa. This study provides the first evidence that the Ap4A-hydrolysing enzyme ApaH is important for P. aeruginosa virulence, highlighting this protein as a novel potential target for antivirulence therapies against P. aeruginosa.
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Affiliation(s)
| | | | - Giulia Ferri
- Department of Medical, Oral and Biotechnology Sciences, University of Chieti-Pescara, Chieti, Italy
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Antonio Recchiuti
- Department of Medical, Oral and Biotechnology Sciences, University of Chieti-Pescara, Chieti, Italy
| | - Francesco Imperi
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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2
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Jin Y, Ke J, Zheng P, Zhang H, Zhu Z, Niu L. Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia. Structure 2024; 32:1197-1207.e4. [PMID: 38701795 DOI: 10.1016/j.str.2024.04.009] [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: 06/21/2023] [Revised: 12/14/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
In this report, we structurally and biochemically characterized the unknown gene product SP1746 from Streptococcus pneumoniae serotype 4. Various crystal structures of SP1746 in the apo form and in complex with different nucleotides were determined. SP1746 is a globular protein, which belongs to the histidine-aspartate (HD) domain superfamily with two Fe3+ ions in the active site that are coordinated by key active site residues and water molecules. All nucleotides bind in a similar orientation in the active site with their phosphate groups anchored to the diiron cluster. Biochemically, SP1746 hydrolyzes different nucleotide substrates. SP1746 most effectively hydrolyzes diadenosine tetraphosphate (Ap4A) to two ADPs. Based on the aforementioned data, we annotated SP1746 as an Ap4A hydrolase, belonging to the YqeK family. Our in vitro data indicate a potential role for SP1746 in regulating Ap4A homeostasis, which requires validation with in vivo experiments in bacteria in the future.
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Affiliation(s)
- Yuping Jin
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jiyuan Ke
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, 4090 Susong Rd, Hefei, Hefei Economic and Technological Development Zone, Hefei, Anhui 230601, China.
| | - Peiyi Zheng
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Haiyan Zhang
- Core Facility Center for Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Zhongliang Zhu
- Core Facility Center for Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Liwen Niu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
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3
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Husain RA, Jiao X, Hennings JC, Giesecke J, Palsule G, Beck-Wödl S, Osmanović D, Bjørgo K, Mir A, Ilyas M, Abbasi SM, Efthymiou S, Dominik N, Maroofian R, Houlden H, Rankin J, Pagnamenta AT, Nashabat M, Altwaijri W, Alfadhel M, Umair M, Khouj E, Reardon W, El-Hattab AW, Mekki M, Houge G, Beetz C, Bauer P, Putoux A, Lesca G, Sanlaville D, Alkuraya FS, Taylor RW, Mentzel HJ, Hübner CA, Huppke P, Hart RP, Haack TB, Kiledjian M, Rubio I. Biallelic NUDT2 variants defective in mRNA decapping cause a neurodevelopmental disease. Brain 2024; 147:1197-1205. [PMID: 38141063 PMCID: PMC10994549 DOI: 10.1093/brain/awad434] [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] [Received: 07/12/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Dysfunctional RNA processing caused by genetic defects in RNA processing enzymes has a profound impact on the nervous system, resulting in neurodevelopmental conditions. We characterized a recessive neurological disorder in 18 children and young adults from 10 independent families typified by intellectual disability, motor developmental delay and gait disturbance. In some patients peripheral neuropathy, corpus callosum abnormalities and progressive basal ganglia deposits were present. The disorder is associated with rare variants in NUDT2, a mRNA decapping and Ap4A hydrolysing enzyme, including novel missense and in-frame deletion variants. We show that these NUDT2 variants lead to a marked loss of enzymatic activity, strongly implicating loss of NUDT2 function as the cause of the disorder. NUDT2-deficient patient fibroblasts exhibit a markedly altered transcriptome, accompanied by changes in mRNA half-life and stability. Amongst the most up-regulated mRNAs in NUDT2-deficient cells, we identified host response and interferon-responsive genes. Importantly, add-back experiments using an Ap4A hydrolase defective in mRNA decapping highlighted loss of NUDT2 decapping as the activity implicated in altered mRNA homeostasis. Our results confirm that reduction or loss of NUDT2 hydrolase activity is associated with a neurological disease, highlighting the importance of a physiologically balanced mRNA processing machinery for neuronal development and homeostasis.
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Affiliation(s)
- Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Jan Giesecke
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
| | - Geeta Palsule
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Stefanie Beck-Wödl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Dina Osmanović
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Kathrine Bjørgo
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Asif Mir
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Muhammad Ilyas
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Saad M Abbasi
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Hospital, Exeter, EX1 2ED, UK
| | - Alistair T Pagnamenta
- Oxford NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Marwan Nashabat
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Waleed Altwaijri
- Department of Pediatrics, Neurology Division, King Abdullah Specialist Children’s Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | | | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates
- Department of Pediatrics, University Hospital Sharjah, 72772, Sharjah, United Arab Emirates
| | - Mohammed Mekki
- Department of Pediatrics, University Hospital Sharjah, 72772, Sharjah, United Arab Emirates
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | | | | | - Audrey Putoux
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Équipe GENDEV, Centre de Recherche en Neurosciences de Lyon, Univ Lyon, Univ Lyon 1, INSERM U1028 CNRS UMR5292, 69008 Lyon, France
| | - Gaetan Lesca
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Physiopathologie et Génétique du Neurone et du Muscle, Univ Lyon, Univ Lyon 1, CNRS, INSERM, UMR5261, U1315, Institut NeuroMyoGène, 69008 Lyon, France
| | - Damien Sanlaville
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Physiopathologie et Génétique du Neurone et du Muscle, Univ Lyon, Univ Lyon 1, CNRS, INSERM, UMR5261, U1315, Institut NeuroMyoGène, 69008 Lyon, France
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Hans-Joachim Mentzel
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
- Section of Pediatric Radiology, Department of Radiology, Jena University Hospital, 07747 Jena, Germany
| | - Christian A Hübner
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Peter Huppke
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Ignacio Rubio
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
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4
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Ben Toumia I, Bachetti T, Chekir-Ghedira L, Profumo A, Ponassi M, Di Domizio A, Izzotti A, Sciacca S, Puglisi C, Forte S, Giuffrida R, Colarossi C, Milardi D, Grasso G, Lanza V, Fiordoro S, Drago G, Tkachenko K, Cardinali B, Romano P, Iervasi E, Vargas GC, Barboro P, Kohnke FH, Rosano C. Fraisinib: a calixpyrrole derivative reducing A549 cell-derived NSCLC tumor in vivo acts as a ligand of the glycine-tRNA synthase, a new molecular target in oncology. Front Pharmacol 2024; 14:1258108. [PMID: 38235113 PMCID: PMC10791888 DOI: 10.3389/fphar.2023.1258108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024] Open
Abstract
Background and purpose: Lung cancer is the leading cause of death in both men and women, constituting a major public health problem worldwide. Non-small-cell lung cancer accounts for 85%-90% of all lung cancers. We propose a compound that successfully fights tumor growth in vivo by targeting the enzyme GARS1. Experimental approach: We present an in-depth investigation of the mechanism through which Fraisinib [meso-(p-acetamidophenyl)-calix(4)pyrrole] affects the human lung adenocarcinoma A549 cell line. In a xenografted model of non-small-cell lung cancer, Fraisinib was found to reduce tumor mass volume without affecting the vital parameters or body weight of mice. Through a computational approach, we uncovered that glycyl-tRNA synthetase is its molecular target. Differential proteomics analysis further confirmed that pathways regulated by Fraisinib are consistent with glycyl-tRNA synthetase inhibition. Key results: Fraisinib displays a strong anti-tumoral potential coupled with limited toxicity in mice. Glycyl-tRNA synthetase has been identified and validated as a protein target of this compound. By inhibiting GARS1, Fraisinib modulates different key biological processes involved in tumoral growth, aggressiveness, and invasiveness. Conclusion and implications: The overall results indicate that Fraisinib is a powerful inhibitor of non-small-cell lung cancer growth by exerting its action on the enzyme GARS1 while displaying marginal toxicity in animal models. Together with the proven ability of this compound to cross the blood-brain barrier, we can assess that Fraisinib can kill two birds with one stone: targeting the primary tumor and its metastases "in one shot." Taken together, we suggest that inhibiting GARS1 expression and/or GARS1 enzymatic activity may be innovative molecular targets for cancer treatment.
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Affiliation(s)
| | | | - Leila Chekir-Ghedira
- Unit of Bioactive Natural Substances and Biotechnology, Faculty of Dental Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Aldo Profumo
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Marco Ponassi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Alberto Izzotti
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Stefano Forte
- Istituto Oncologico del Mediterraneo, Viagrande, Italy
| | | | | | - Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Valeria Lanza
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Stefano Fiordoro
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Giacomo Drago
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Paolo Romano
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Erika Iervasi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Paola Barboro
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Franz Heinrich Kohnke
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), University of Messina, Messina, Italy
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5
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Dobrogojski J, Nguyen VH, Kowalska J, Borek S, Pietrowska-Borek M. The Plasma Membrane Purinoreceptor P2K1/DORN1 Is Essential in Stomatal Closure Evoked by Extracellular Diadenosine Tetraphosphate (Ap 4A) in Arabidopsis thaliana. Int J Mol Sci 2023; 24:16688. [PMID: 38069010 PMCID: PMC10706190 DOI: 10.3390/ijms242316688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Dinucleoside polyphosphates (NpnNs) are considered novel signalling molecules involved in the induction of plant defence mechanisms. However, NpnN signal recognition and transduction are still enigmatic. Therefore, the aim of our research was the identification of the NpnN receptor and signal transduction pathways evoked by these nucleotides. Earlier, we proved that purine and pyrimidine NpnNs differentially affect the phenylpropanoid pathway in Vitis vinifera suspension-cultured cells. Here, we report, for the first time, that both diadenosine tetraphosphate (Ap4A) and dicytidine tetraphosphate (Cp4C)-induced stomatal closure in Arabidopsis thaliana. Moreover, we showed that plasma membrane purinoreceptor P2K1/DORN1 (does not respond to nucleotide 1) is essential for Ap4A-induced stomata movements but not for Cp4C. Wild-type Col-0 and the dorn1-3 A. thaliana knockout mutant were used. Examination of the leaf epidermis dorn1-3 mutant provided evidence that P2K1/DORN1 is a part of the signal transduction pathway in stomatal closure evoked by extracellular Ap4A but not by Cp4C. Reactive oxygen species (ROS) are involved in signal transduction caused by Ap4A and Cp4C, leading to stomatal closure. Ap4A induced and Cp4C suppressed the transcriptional response in wild-type plants. Moreover, in dorn1-3 leaves, the effect of Ap4A on gene expression was impaired. The interaction between P2K1/DORN1 and Ap4A leads to changes in the transcription of signalling hubs in signal transduction pathways.
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Affiliation(s)
- Jędrzej Dobrogojski
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Van Hai Nguyen
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (V.H.N.); (J.K.)
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (V.H.N.); (J.K.)
| | - Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
| | - Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
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6
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Ji X, Yu R, Zhu M, Zhang C, Zhou L, Cai T, Li W. Diadenosine tetraphosphate modulated quorum sensing in bacteria treated with kanamycin. BMC Microbiol 2023; 23:353. [PMID: 37978430 PMCID: PMC10657157 DOI: 10.1186/s12866-023-03113-3] [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] [Received: 09/14/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The dinucleotide alarmone diadenosine tetraphosphate (Ap4A), which is found in cells, has been shown to affect the survival of bacteria under stress. RESULTS Here, we labeled Ap4A with biotin and incubated the labeled Ap4A with the total proteins extracted from kanamycin-treated Escherichia coli to identify the Ap4A binding protein in bacteria treated with kanamycin. Liquid chromatography‒mass spectrometry (LCMS) and bioinformatics were used to identify novel proteins that Ap4A interacts with that are involved in biofilm formation, quorum sensing, and lipopolysaccharide biosynthesis pathways. Then, we used the apaH knockout strain of E. coli K12-MG1655, which had increased intracellular Ap4A, to demonstrate that Ap4A affected the expression of genes in these three pathways. We also found that the swarming motility of the apaH mutant strain was reduced compared with that of the wild-type strain, and under kanamycin treatment, the biofilm formation of the mutant strain decreased. CONCLUSIONS These results showed that Ap4A can reduce the survival rate of bacteria treated with kanamycin by regulating quorum sensing (QS). These effects can expand the application of kanamycin combinations in the treatment of multidrug-resistant bacteria.
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Affiliation(s)
- Xia Ji
- School of Life Science, Huizhou University, Huizhou, 516007, China.
| | - Ruojing Yu
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Meilian Zhu
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Cuilin Zhang
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Libin Zhou
- School of Life Science, Huizhou University, Huizhou, 516007, China
| | - Tianshu Cai
- Huizhou Health Sciences Polytechnic, Huizhou, 516025, China
| | - Weiwei Li
- Huizhou Health Sciences Polytechnic, Huizhou, 516025, China
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7
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Tischlik S, Oelker M, Rogne P, Sauer-Eriksson AE, Drescher M, Wolf-Watz M. Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by E. coli Adenylate Kinase. Biochemistry 2023; 62:2238-2243. [PMID: 37418448 PMCID: PMC10399197 DOI: 10.1021/acs.biochem.3c00189] [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: 04/12/2023] [Revised: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Adenylate kinases play a crucial role in cellular energy homeostasis through the interconversion of ATP, AMP, and ADP in all living organisms. Here, we explore how adenylate kinase (AdK) from Escherichia coli interacts with diadenosine tetraphosphate (AP4A), a putative alarmone associated with transcriptional regulation, stress, and DNA damage response. From a combination of EPR and NMR spectroscopy together with X-ray crystallography, we found that AdK interacts with AP4A with two distinct modes that occur on disparate time scales. First, AdK dynamically interconverts between open and closed states with equal weights in the presence of AP4A. On a much slower time scale, AdK hydrolyses AP4A, and we suggest that the dynamically accessed substrate-bound open AdK conformation enables this hydrolytic activity. The partitioning of the enzyme into open and closed states is discussed in relation to a recently proposed linkage between active site dynamics and collective conformational dynamics.
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Affiliation(s)
- Sonja Tischlik
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Melanie Oelker
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Per Rogne
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - A. Elisabeth Sauer-Eriksson
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
- Centre
of Microbial Research (UCMR), Umeå
University, SE-901 87 Umeå, Sweden
| | - Malte Drescher
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Magnus Wolf-Watz
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
- Centre
of Microbial Research (UCMR), Umeå
University, SE-901 87 Umeå, Sweden
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8
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Zhao H, Ding T, Chen Y, Yang W, Rao J, Liu D, Yi B. Arecoline aggravates acute ulcerative colitis in mice by affecting intestinal microbiota and serum metabolites. Front Immunol 2023; 14:1197922. [PMID: 37492574 PMCID: PMC10363717 DOI: 10.3389/fimmu.2023.1197922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 07/27/2023] Open
Abstract
Arecoline is an alkaloid extracted from betel nut, which has various pharmacological effects. In the present study, we showed that arecoline aggravated experimental acute ulcerative colitis (UC) induced by dextran sodium sulfate (DSS) in mice. We measured body weight and colon length, evaluated disease activity index, colon pathology sections, and levels of colonic inflammatory factors. Arecoline exacerbated the clinical signs of UC and the colonic inflammatory response in mice. The results of 16S rRNA sequencing of fecal samples showed a significant decrease in the percentage of probiotic bacteria Ligilactobacillus, Limosilactobacillus and Lactobacillus and a significant increase in the percentage of conditionally pathogenic bacteria Odoribacter and Bacteroides after arecoline treatment. Serum untargeted metabolomics showed that arecoline intervention reduced the levels of ergothioneine, pentostatin, diadenosine tetraphosphate and other metabolites and modulated nicotinate and nicotinamide metabolism, metabolic pathways, glyoxylate and dicarboxylate metabolism, and other metabolic pathways of intestinal microorganisms. According to the combined microbial and metabolite analysis, arecoline influences metabolite levels by modulating the intestinal microbiota. In summary, it was found that arecoline treatment exacerbated colonic injury and intestinal inflammatory responses in UC mice, disrupted the host's intestinal flora, and affected changes in flora metabolites, thereby exacerbating the development of colonic inflammation. Therefore, the consumption of betel nut can be associated with the risk of aggravating UC.
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Affiliation(s)
- Hu Zhao
- School of Pharmacy, Nanchang University, Nanchang, China
- 2nd Abdominal Surgery Department, Jiangxi Cancer Hospital, Nanchang, China
| | - Taohui Ding
- School of Pharmacy, Nanchang University, Nanchang, China
- 2nd Abdominal Surgery Department, Jiangxi Cancer Hospital, Nanchang, China
| | - Yanglin Chen
- 2nd Abdominal Surgery Department, Jiangxi Cancer Hospital, Nanchang, China
| | - Wenbin Yang
- School of Pharmacy, Nanchang University, Nanchang, China
| | - Jun Rao
- 2nd Abdominal Surgery Department, Jiangxi Cancer Hospital, Nanchang, China
| | - Dan Liu
- School of Pharmacy, Nanchang University, Nanchang, China
| | - Bo Yi
- 2nd Abdominal Surgery Department, Jiangxi Cancer Hospital, Nanchang, China
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9
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Zheng T, Jing M, Gong T, Yan J, Wang X, Xu M, Zhou X, Zeng J, Li Y. Regulatory mechanisms of exopolysaccharide synthesis and biofilm formation in Streptococcus mutans. J Oral Microbiol 2023; 15:2225257. [PMID: 37346997 PMCID: PMC10281425 DOI: 10.1080/20002297.2023.2225257] [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: 11/21/2022] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023] Open
Abstract
Background Dental caries is a chronic, multifactorial and biofilm-mediated oral bacterial infection affecting almost every age group and every geographical region. Streptococcus mutans is considered an important pathogen responsible for the initiation and development of dental caries. It produces exopolysaccharides in situ to promote the colonization of cariogenic bacteria and coordinate dental biofilm development. Objective The understanding of the regulatory mechanism of S. mutans biofilm formation can provide a theoretical basis for the prevention and treatment of caries. Design At present, an increasing number of studies have identified many regulatory systems in S. mutans that regulate biofilm formation, including second messengers (e.g. c-di-AMP, Ap4A), transcription factors (e.g. EpsR, RcrR, StsR, AhrC, FruR), two-component systems (e.g. CovR, VicR), small RNA (including sRNA0426, srn92532, and srn133489), acetylation modifications (e.g. ActG), CRISPR-associated proteins (e.g. Cas3), PTS systems (e.g. EIIAB), quorum-sensing signaling system (e.g. LuxS), enzymes (including Dex, YidC, CopZ, EzrA, lmrB, SprV, RecA, PdxR, MurI) and small-molecule metabolites. Results This review summarizes the recent progress in the molecular regulatory mechanisms of exopolysaccharides synthesis and biofilm formation in S. mutans.
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Affiliation(s)
- Ting Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Meiling Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiangchuan Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mai Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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10
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van der Does C, Braun F, Ren H, Albers SV. Putative nucleotide-based second messengers in archaea. MICROLIFE 2023; 4:uqad027. [PMID: 37305433 PMCID: PMC10249747 DOI: 10.1093/femsml/uqad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/07/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.
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Affiliation(s)
- Chris van der Does
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hongcheng Ren
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
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11
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Zegarra V, Mais CN, Freitag J, Bange G. The mysterious diadenosine tetraphosphate (AP4A). MICROLIFE 2023; 4:uqad016. [PMID: 37223742 PMCID: PMC10148737 DOI: 10.1093/femsml/uqad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
Dinucleoside polyphosphates, a class of nucleotides found amongst all the Trees of Life, have been gathering a lot of attention in the past decades due to their putative role as cellular alarmones. In particular, diadenosine tetraphosphate (AP4A) has been widely studied in bacteria facing various environmental challenges and has been proposed to be important for ensuring cellular survivability through harsh conditions. Here, we discuss the current understanding of AP4A synthesis and degradation, protein targets, their molecular structure where possible, and insights into the molecular mechanisms of AP4A action and its physiological consequences. Lastly, we will briefly touch on what is known with regards to AP4A beyond the bacterial kingdom, given its increasing appearance in the eukaryotic world. Altogether, the notion that AP4A is a conserved second messenger in organisms ranging from bacteria to humans and is able to signal and modulate cellular stress regulation seems promising.
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Affiliation(s)
- Victor Zegarra
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Johannes Freitag
- Department of Biology, Philipps University Marburg, Marburg 35043, Germany
| | - Gert Bange
- Corresponding author. Karl-von-Frisch Strasse 14, 35043 Marburg, Germany. E-mail:
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12
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Singh S, Anand R. Diverse strategies adopted by nature for regulating purine biosynthesis via fine-tuning of purine metabolic enzymes. Curr Opin Chem Biol 2023; 73:102261. [PMID: 36682088 DOI: 10.1016/j.cbpa.2022.102261] [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: 08/30/2022] [Revised: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023]
Abstract
Purine nucleotides, generated by de novo synthesis and salvage pathways, are essential for metabolism and act as building blocks of genetic material. To avoid an imbalance in the nucleotide pool, nature has devised several strategies to regulate/tune the catalytic performance of key purine metabolic enzymes. Here, we discuss some recent examples, such as stress-regulating alarmones that bind to select pathway enzymes, huge ensembles like dynamic metabolons and self-assembled filaments that highlight the layered fine-control prevalent in the purine metabolic pathway to fulfill requisite purine demands. Examples of enzymes that turn-on only under allosteric control, are regulated via long-distance communication that facilitates transient conduits have additionally been explored.
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Affiliation(s)
- Sukhwinder Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; DBT-Wellcome Trust India Alliance Senior Fellow, Mumbai 400076, India.
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13
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Leiva LE, Zegarra V, Bange G, Ibba M. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria. Microbiol Mol Biol Rev 2023; 87:e0004422. [PMID: 36853029 PMCID: PMC10029340 DOI: 10.1128/mmbr.00044-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
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14
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Frese M, Saumer P, Yuan Y, Herzog D, Höpfner D, Itzen A, Marx A. The Alarmone Diadenosine Tetraphosphate as a Cosubstrate for Protein AMPylation. Angew Chem Int Ed Engl 2023; 62:e202213279. [PMID: 36524454 PMCID: PMC10107192 DOI: 10.1002/anie.202213279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Diadenosine polyphosphates (Apn As) are non-canonical nucleotides whose cellular concentrations increase during stress and are therefore termed alarmones, signaling homeostatic imbalance. Their cellular role is poorly understood. In this work, we assessed Apn As for their usage as cosubstrates for protein AMPylation, a post-translational modification in which adenosine monophosphate (AMP) is transferred to proteins. In humans, AMPylation mediated by the AMPylator FICD with ATP as a cosubstrate is a response to ER stress. Herein, we demonstrate that Ap4 A is proficiently consumed for AMPylation by FICD. By chemical proteomics using a new chemical probe, we identified new potential AMPylation targets. Interestingly, we found that AMPylation targets of FICD may differ depending on the nucleotide cosubstrate. These results may suggest that signaling at elevated Ap4 A levels during cellular stress differs from when Ap4 A is present at low concentrations, allowing response to extracellular cues.
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Affiliation(s)
- Matthias Frese
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Philip Saumer
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Yizhi Yuan
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Doreen Herzog
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.,Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.,Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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15
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Regulatory Landscape of the Pseudomonas aeruginosa Phosphoethanolamine Transferase Gene eptA in the Context of Colistin Resistance. Antibiotics (Basel) 2023; 12:antibiotics12020200. [PMID: 36830112 PMCID: PMC9952513 DOI: 10.3390/antibiotics12020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa has the genetic potential to acquire colistin resistance through the modification of lipopolysaccharide by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) or phosphoethanolamine (PEtN), mediated by the arn operon or the eptA gene, respectively. However, in vitro evolution experiments and genetic analysis of clinical isolates indicate that lipopolysaccharide modification with L-Ara4N is invariably preferred over PEtN addition as the colistin resistance mechanism in this bacterium. Since little is known about eptA regulation in P. aeruginosa, we generated luminescent derivatives of the reference strain P. aeruginosa PAO1 to monitor arn and eptA promoter activity. We performed transposon mutagenesis assays to compare the likelihood of acquiring mutations leading to arn or eptA induction and to identify eptA regulators. The analysis revealed that eptA was slightly induced under certain stress conditions, such as arginine or biotin depletion and accumulation of the signal molecule diadenosine tetraphosphate, but the induction did not confer colistin resistance. Moreover, we demonstrated that spontaneous mutations leading to colistin resistance invariably triggered arn rather than eptA expression, and that eptA was not induced in resistant mutants upon colistin exposure. Overall, these results suggest that the contribution of eptA to colistin resistance in P. aeruginosa may be limited by regulatory restraints.
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16
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Chauhan SS, Weinert EE. Generation of nucleotide-linked resins for identification of novel binding proteins. Methods Enzymol 2023; 679:323-330. [PMID: 36682867 DOI: 10.1016/bs.mie.2022.08.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Organisms use numerous nucleotide-containing compounds as intracellular signals to control behavior. Identifying the biomolecules responsible to sensing and responding to changes in signaling molecule concentration is an important area of research. However, identifying the binding proteins can be challenging when there is no prior information available about binding motifs. In this chapter, we describe a straightforward method to generate nucleotide-linked resins for use in pull-down experiments to identify binding proteins. The protocol outlined in this chapter also can be adapted to generate custom resins linked to other molecules of interest.
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Affiliation(s)
- Shikha S Chauhan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States; Department of Chemistry, Pennsylvania State University, University Park, PA, United States.
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17
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Multi-Omics Analysis Revealed a Significant Alteration of Critical Metabolic Pathways Due to Sorafenib-Resistance in Hep3B Cell Lines. Int J Mol Sci 2022; 23:ijms231911975. [PMID: 36233276 PMCID: PMC9569810 DOI: 10.3390/ijms231911975] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 09/25/2022] [Indexed: 11/09/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the second prominent cause of cancer-associated death worldwide. Usually, HCC is diagnosed in advanced stages, wherein sorafenib, a multiple target tyrosine kinase inhibitor, is used as the first line of treatment. Unfortunately, resistance to sorafenib is usually encountered within six months of treatment. Therefore, there is a critical need to identify the underlying reasons for drug resistance. In the present study, we investigated the proteomic and metabolomics alterations accompanying sorafenib resistance in hepatocellular carcinoma Hep3B cells by employing ultra-high-performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS). The Bruker Human Metabolome Database (HMDB) library was used to identify the differentially abundant metabolites through MetaboScape 4.0 software (Bruker). For protein annotation and identification, the Uniprot proteome for Homo sapiens (Human) database was utilized through MaxQuant. The results revealed that 27 metabolites and 18 proteins were significantly dysregulated due to sorafenib resistance in Hep3B cells compared to the parental phenotype. D-alanine, L-proline, o-tyrosine, succinic acid and phosphatidylcholine (PC, 16:0/16:0) were among the significantly altered metabolites. Ubiquitin carboxyl-terminal hydrolase isozyme L1, mitochondrial superoxide dismutase, UDP-glucose-6-dehydrogenase, sorbitol dehydrogenase and calpain small subunit 1 were among the significantly altered proteins. The findings revealed that resistant Hep3B cells demonstrated significant alterations in amino acid and nucleotide metabolic pathways, energy production pathways and other pathways related to cancer aggressiveness, such as migration, proliferation and drug-resistance. Joint pathway enrichment analysis unveiled unique pathways, including the antifolate resistance pathway and other important pathways that maintain cancer cells' survival, growth, and proliferation. Collectively, the results identified potential biomarkers for sorafenib-resistant HCC and gave insights into their role in chemotherapeutic drug resistance, cancer initiation, progression and aggressiveness, which may contribute to better prognosis and chemotherapeutic outcomes.
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18
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Farache D, Antine SP, Lee ASY. Moonlighting translation factors: multifunctionality drives diverse gene regulation. Trends Cell Biol 2022; 32:762-772. [PMID: 35466028 PMCID: PMC9378348 DOI: 10.1016/j.tcb.2022.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/09/2022]
Abstract
Translation factors have traditionally been viewed as proteins that drive ribosome function and ensure accurate mRNA translation. Recent discoveries have highlighted that these factors can also moonlight in gene regulation, but through functions distinct from their canonical roles in protein synthesis. Notably, the additional functions that translation factors encode are diverse, ranging from transcriptional control and extracellular signaling to RNA binding, and are highly regulated in response to external cues and the intrinsic cellular state. Thus, this multifunctionality of translation factors provides an additional mechanism for exquisite control of gene expression.
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Affiliation(s)
- Dorian Farache
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sadie P Antine
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy S Y Lee
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
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19
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Giammarinaro PI, Young MKM, Steinchen W, Mais CN, Hochberg G, Yang J, Stevenson DM, Amador-Noguez D, Paulus A, Wang JD, Bange G. Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilis. Nat Microbiol 2022; 7:1442-1452. [PMID: 35953658 PMCID: PMC10439310 DOI: 10.1038/s41564-022-01193-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Diadenosine tetraphosphate (Ap4A) is a putative second messenger molecule that is conserved from bacteria to humans. Nevertheless, its physiological role and the underlying molecular mechanisms are poorly characterized. We investigated the molecular mechanism by which Ap4A regulates inosine-5'-monophosphate dehydrogenase (IMPDH, a key branching point enzyme for the biosynthesis of adenosine or guanosine nucleotides) in Bacillus subtilis. We solved the crystal structure of BsIMPDH bound to Ap4A at a resolution of 2.45 Å to show that Ap4A binds to the interface between two IMPDH subunits, acting as the glue that switches active IMPDH tetramers into less active octamers. Guided by these insights, we engineered mutant strains of B. subtilis that bypass Ap4A-dependent IMPDH regulation without perturbing intracellular Ap4A pools themselves. We used metabolomics, which suggests that these mutants have a dysregulated purine, and in particular GTP, metabolome and phenotypic analysis, which shows increased sensitivity of B. subtilis IMPDH mutant strains to heat compared with wild-type strains. Our study identifies a central role for IMPDH in remodelling metabolism and heat resistance, and provides evidence that Ap4A can function as an alarmone.
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Affiliation(s)
- Pietro I Giammarinaro
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Megan K M Young
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Wieland Steinchen
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Georg Hochberg
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Anja Paulus
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gert Bange
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany.
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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20
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Abstract
More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.
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Affiliation(s)
- Ronald R. Breaker
- Corresponding Author: Ronald R. Breaker - Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, United States; Phone: 203-432-9389; , Twitter: @RonBreaker
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21
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Braun F, Recalde A, Bähre H, Seifert R, Albers SV. Putative Nucleotide-Based Second Messengers in the Archaeal Model Organisms Haloferax volcanii and Sulfolobus acidocaldarius. Front Microbiol 2021; 12:779012. [PMID: 34880846 PMCID: PMC8646023 DOI: 10.3389/fmicb.2021.779012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
Research on nucleotide-based second messengers began in 1956 with the discovery of cyclic adenosine monophosphate (3',5'-cAMP) by Earl Wilbur Sutherland and his co-workers. Since then, a broad variety of different signaling molecules composed of nucleotides has been discovered. These molecules fulfill crucial tasks in the context of intracellular signal transduction. The vast majority of the currently available knowledge about nucleotide-based second messengers originates from model organisms belonging either to the domain of eukaryotes or to the domain of bacteria, while the archaeal domain is significantly underrepresented in the field of nucleotide-based second messenger research. For several well-stablished eukaryotic and/or bacterial nucleotide-based second messengers, it is currently not clear whether these signaling molecules are present in archaea. In order to shed some light on this issue, this study analyzed cell extracts of two major archaeal model organisms, the euryarchaeon Haloferax volcanii and the crenarchaeon Sulfolobus acidocaldarius, using a modern mass spectrometry method to detect a broad variety of currently known nucleotide-based second messengers. The nucleotides 3',5'-cAMP, cyclic guanosine monophosphate (3',5'-cGMP), 5'-phosphoadenylyl-3',5'-adenosine (5'-pApA), diadenosine tetraphosphate (Ap4A) as well as the 2',3'-cyclic isomers of all four RNA building blocks (2',3'-cNMPs) were present in both species. In addition, H. volcanii cell extracts also contain cyclic cytosine monophosphate (3',5'-cCMP), cyclic uridine monophosphate (3',5'-cUMP) and cyclic diadenosine monophosphate (3',5'-c-di-AMP). The widely distributed bacterial second messengers cyclic diguanosine monophosphate (3',5'-c-di-GMP) and guanosine (penta-)/tetraphosphate [(p)ppGpp] could not be detected. In summary, this study gives a comprehensive overview on the presence of a large set of currently established or putative nucleotide-based second messengers in an eury- and a crenarchaeal model organism.
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Affiliation(s)
- Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Alejandra Recalde
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
| | - Roland Seifert
- Research Core Unit Metabolomics, Hannover Medical School, Hanover, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
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Zheng T, Jing M, Gong T, Yan J, Zeng J, Li Y. Deletion of the yqeK gene leads to the accumulation of Ap4A and reduced biofilm formation in Streptococcus mutans. Mol Oral Microbiol 2021; 37:9-21. [PMID: 34761536 DOI: 10.1111/omi.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023]
Abstract
Diadenosine-5',5'''-P1, P4-tetraphosphate (Ap4A) is a second messenger playing a crucial role in various life activities of bacteria. The increase of Ap4A expression is pleiotropic, resulting in an impairment in the formation of biofilm and other physiological functions in some bacteria. However, Ap4A function in Streptococcus mutans, an important pathogen related to dental caries, remains unknown. In this work, the Ap4A hydrolase, YqeK, was identified and characterized in S. mutans. Then, the effects of yqeK deletion on the growth, biofilm formation, and exopolysaccharide (EPS) quantification in S. mutans were determined by the assessment of the growth curve, crystal violet, and anthrone-sulfuric acid, respectively, and visualized by microscopy. The results showed that the in-frame deletion of the yqeK gene in S. mutans UA159 led to an increase in Ap4A levels, lag phase in the early growth, as well as decrease in biofilm formation and water-insoluble exopolysaccharide production. Global gene expression profile showed that the expression of 88 genes was changed in the yqeK mutant, and among these, 42 were upregulated and 46 were downregulated when compared with the wild-type S. mutans UA159. Upregulated genes were mainly involved in post-translational modification, protein turnover, and chaperones, while downregulated genes were mainly involved in carbohydrate transport and metabolism. Important virulence genes related to biofilms, such as gtfB, gtfC, and gbpC, were also significantly downregulated. In conclusion, these results indicated that YqeK affected the formation of biofilms and the expression of biofilm-related genes in S. mutans.
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Affiliation(s)
- Ting Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Meiling Jing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiangchuan Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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