1
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Cong D, Steinbuch KB, Koyama R, Lam TV, Lam JY, Tor Y. Site-specific RNA modification via initiation of in vitro transcription reactions with m 6A and isomorphic emissive adenosine analogs. RSC Chem Biol 2024; 5:454-458. [PMID: 38725913 PMCID: PMC11078205 DOI: 10.1039/d4cb00045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/27/2024] [Indexed: 05/12/2024] Open
Abstract
The templated enzymatic incorporation of adenosine and its analogs, including m6A, thA and tzA into RNA transcripts, has been explored. Enforced transcription initiation with excess free nucleosides and the native triphosphates generates 5'-end modified transcripts, which can be 5'-phosphorylated and ligated to provide full length, singly modified RNA oligomers. To explore structural integrity, functionality and utility of the resulting non-canonical purine-containing RNA constructs, a MazF RNA hairpin substrate has been synthesized and analyzed for its susceptibility to this endonuclease. Additionally, RNA substrates, containing a singly incorporated isomorphic emissive nucleoside, can be used to monitor the enzymatic reactions in real-time by steady state fluorescence spectroscopy.
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Affiliation(s)
- Deyuan Cong
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093-0358 USA
| | - Kfir B Steinbuch
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093-0358 USA
| | - Ryosuke Koyama
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093-0358 USA
| | - Tyler V Lam
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093-0358 USA
| | - Jamie Y Lam
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093-0358 USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla California 92093-0358 USA
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2
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Okabe T, Aoi R, Yokota A, Tamiya-Ishitsuka H, Jiang Y, Sasaki A, Tsuneda S, Noda N. Arg-73 of the RNA endonuclease MazF in Salmonella enterica subsp. arizonae contributes to guanine and uracil recognition in the cleavage sequence. J Biol Chem 2024; 300:105636. [PMID: 38199572 PMCID: PMC10864209 DOI: 10.1016/j.jbc.2024.105636] [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: 10/26/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The sequence-specific endoribonuclease MazF is widely conserved among prokaryotes. Approximately 20 different MazF cleavage sequences have been discovered, varying from three to seven nucleotides in length. Although MazFs from various prokaryotes were found, the cleavage sequences of most MazFs are unknown. Here, we characterized the conserved MazF of Salmonella enterica subsp. arizonae (MazF-SEA). Using massive parallel sequencing and fluorometric assays, we revealed that MazF-SEA preferentially cleaves the sequences U∧ACG and U∧ACU (∧ represents cleavage sites). In addition, we predicted the 3D structure of MazF-SEA using AlphaFold2 and aligned it with the crystal structure of RNA-bound Bacillus subtilis MazF to evaluate RNA interactions. We found Arg-73 of MazF-SEA interacts with RNAs containing G and U at the third position from the cleavage sites (U∧ACG and U∧ACU). We then obtained the mutated MazF-SEA R73L protein to evaluate the significance of Arg-73 interaction with RNAs containing G and U at this position. We also used fluorometric and kinetic assays and showed the enzymatic activity of MazF-SEA R73L for the sequence UACG and UACU was significantly decreased. These results suggest Arg-73 is essential for recognizing G and U at the third position from the cleavage sites. This is the first study to our knowledge to identify a single residue responsible for RNA recognition by MazF. Owing to its high specificity and ribosome-independence, MazF is useful for RNA cleavage in vitro. These results will likely contribute to increasing the diversity of MazF specificity and to furthering the application of MazF in RNA engineering.
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Affiliation(s)
- Takuma Okabe
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Rie Aoi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Hiroko Tamiya-Ishitsuka
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Yunong Jiang
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan; Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki, Japan
| | - Akira Sasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan; School of Integrative and Global Majors, University of Tsukuba, Ibaraki, Japan.
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3
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Cao G, Deng Y, Chen X, Huo D, Li J, Yang M, Hou C. The fluorescent biosensor for detecting N 6 methyladenine FzD5 mRNA and MazF activity. Anal Chim Acta 2021; 1188:339185. [PMID: 34794576 DOI: 10.1016/j.aca.2021.339185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 01/11/2023]
Abstract
N6 methyladenine (m6A) modification of the FzD5 mRNA, an important post-transcriptional regulation in eukaryotes, is closely related to the occurrence and development of breast cancer. Here, we developed an ultra-sensitive biosensor based on MazF combining with cascaded strand displacement amplification (C-SDA) and CRISPR/Cas12a to detect m6A FzD5 mRNA. MazF toxin protein is a vital component of the bacterial mazEF toxin-antitoxin system that is sensitive to m6A RNA. Take advantage of it, the biosensor achieved antibody-independent and gene-specific detection for m6A RNA. Moreover, compared with traditional amplification methods, the more efficient C-SDA and the CRISPR/Cas12a system with trans-cleavage activity gave the fluorescent biosensor an excellent sensitivity with the detection limit of 0.64 fM. In addition, MazF, as a new antibacterial target, was detected by the biosensor based on C-SDA and CRISPR/Cas12a with the detection limit of 1.127 × 10-4 U mL-1. More importantly, the biosensor has good performance in complex samples. Therefore, the biosensor is a potential tool in detecting m6A FzD5 mRNA and MazF activity.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Yuanyi Deng
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Xiaolong Chen
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Danqun Huo
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China
| | - Jiawei Li
- Chongqing University Three Gorges Hospital, Chongqing, 404000, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
| | - Mei Yang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Changjun Hou
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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4
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Tamiya-Ishitsuka H, Tsuruga M, Noda N, Yokota A. Conserved Amino Acid Moieties of Candidatus Desulforudis audaxviator MazF Determine Ribonuclease Activity and Specificity. Front Microbiol 2021; 12:748619. [PMID: 34867867 PMCID: PMC8634880 DOI: 10.3389/fmicb.2021.748619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
The toxin-antitoxin (TA) system, inherent to various prokaryotes, plays a critical role in survival and adaptation to diverse environmental stresses. The toxin MazF, belonging to the type II TA system, functions as a sequence-specific ribonuclease that recognizes 3 to 7 bases. In recent studies, crystallographic analysis of MazFs from several species have suggested the presence of amino acid sites important for MazF substrate RNA binding and for its catalytic activity. Herein, we characterized MazF obtained from Candidatus Desulforudis audaxviator (MazF-Da) and identified the amino acid residues necessary for its catalytic function. MazF-Da, expressed using a cell-free protein synthesis system, is a six-base-recognition-specific ribonuclease that preferentially cleaves UACAAA sequences and weakly cleaves UACGAA and UACUAA sequences. We found that MazF-Da exhibited the highest activity at around 60°C. Analysis using mutants with a single mutation at an amino acid residue site that is well conserved across various MazF toxins showed that G18, E20, R25, and P26 were important for the ribonuclease activity of MazF-Da. The recognition sequence of the N36A mutant differed from that of the wild type. This mutant cleaved UACAAG sequences in addition to UACAAA sequences, but did not cleave UACGAA or UACUAA sequences, suggesting that Asn36 affects the loosening and narrowing of MazF-Da cleavage sequence recognition. Our study posits UACAAA as the recognition sequence of MazF-Da and provides insight into the amino acid sites that are key to its unique enzymatic properties.
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Affiliation(s)
- Hiroko Tamiya-Ishitsuka
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masako Tsuruga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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5
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MazF Endoribonucleolytic Toxin Conserved in Nitrospira Specifically Cleaves the AACU, AACG, and AAUU Motifs. Toxins (Basel) 2020; 12:toxins12050287. [PMID: 32365819 PMCID: PMC7291052 DOI: 10.3390/toxins12050287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 11/27/2022] Open
Abstract
MazF is an endoribonucleolytic toxin that cleaves intracellular RNAs in sequence-specific manners. It is liberated in bacterial cells in response to environmental changes and is suggested to contribute to bacterial survival by inducing translational regulation. Thus, determining the cleavage specificity provides insights into the physiological functions of MazF orthologues. Nitrospira, detected in a wide range of environments, is thought to have evolved the ability to cope with their surroundings. To investigate the molecular mechanism of its environmental adaption, a MazF module from Nitrospira strain ND1, which was isolated from the activated sludge of a wastewater treatment plant, is examined in this study. By combining a massive parallel sequencing method and fluorometric assay, we detected that this functional RNA-cleaving toxin specifically recognizes the AACU, AACG, and AAUU motifs. Additionally, statistical analysis suggested that this enzyme regulates various specific functions in order to resist environmental stresses.
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6
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Waduge P, Sati GC, Crich D, Chow CS. Use of a fluorescence assay to determine relative affinities of semisynthetic aminoglycosides to small RNAs representing bacterial and mitochondrial A sites. Bioorg Med Chem 2019; 27:115121. [PMID: 31610941 PMCID: PMC6961810 DOI: 10.1016/j.bmc.2019.115121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/02/2019] [Accepted: 09/12/2019] [Indexed: 10/26/2022]
Abstract
The off-target binding of aminoglycosides (AGs) to the A site of human mitochondrial ribosomes in addition to bacterial ribosomes causes ototoxicity and limits their potential as antibiotics. A fluorescence assay was employed to determine relative binding affinities of classical and improved AG compounds to synthetic RNA constructs representing the bacterial and mitochondrial A sites. Results compared well with previously reported in vitro translation assays with engineered ribosomes. Therefore, the minimal RNA motifs and fluorescence assay are shown here to be useful for assessing the selectivity of new compounds.
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Affiliation(s)
- Prabuddha Waduge
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Girish C Sati
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - David Crich
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
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7
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Kwapong AA, Stapleton P, Gibbons S. Inhibiting plasmid mobility: The effect of isothiocyanates on bacterial conjugation. Int J Antimicrob Agents 2019; 53:629-636. [PMID: 30685311 DOI: 10.1016/j.ijantimicag.2019.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/12/2018] [Accepted: 01/20/2019] [Indexed: 01/13/2023]
Abstract
Bacterial conjugation is the main mechanism for the transfer of multiple antimicrobial resistance genes among pathogenic micro-organisms. This process may be controlled by compounds that inhibit bacterial conjugation. In this study, the effects of allyl isothiocyanate, l-sulforaphane, benzyl isothiocyanate, phenylethyl isothiocyanate and 4-methoxyphenyl isothiocyanate on the conjugation of broad-host-range plasmids harbouring various antimicrobial resistance genes in Escherichia coli were investigated, namely plasmids pKM101 (IncN), TP114 (IncI2), pUB307 (IncP) and the low-copy-number plasmid R7K (IncW). Benzyl isothiocyanate (32 mg/L) significantly reduced conjugal transfer of pKM101, TP114 and pUB307 to 0.3 ± 0.6%, 10.7 ± 3.3% and 6.5 ± 1.0%, respectively. l-sulforaphane (16 mg/L; transfer frequency 21.5 ± 5.1%) and 4-methoxyphenyl isothiocyanate (100 mg/L; transfer frequency 5.2 ± 2.8%) were the only compounds showing anti-conjugal specificity by actively reducing the transfer of R7K and pUB307, respectively.
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Affiliation(s)
- Awo Afi Kwapong
- Research Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; Department of Pharmaceutics and Microbiology, School of Pharmacy, University of Ghana, Accra, Ghana
| | - Paul Stapleton
- Research Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Simon Gibbons
- Research Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK.
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8
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Miyamoto T, Yokota A, Ota Y, Tsuruga M, Aoi R, Tsuneda S, Noda N. Nitrosomonas europaea MazF Specifically Recognises the UGG Motif and Promotes Selective RNA Degradation. Front Microbiol 2018; 9:2386. [PMID: 30349517 PMCID: PMC6186784 DOI: 10.3389/fmicb.2018.02386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/18/2018] [Indexed: 01/08/2023] Open
Abstract
Toxin-antitoxin (TA) systems are implicated in prokaryotic stress adaptation. Previously, bioinformatics analysis predicted that such systems are abundant in some slowly growing chemolithotrophs; e.g., Nitrosomonas europaea. Nevertheless, the molecular functions of these stress-response modules remain largely unclear, limiting insight regarding their physiological roles. Herein, we show that one of the putative MazF family members, encoded at the ALW85_RS04820 locus, constitutes a functional toxin that engenders a TA pair with its cognate MazE antitoxin. The coordinate application of a specialised RNA-Seq and a fluorescence quenching technique clarified that a unique triplet, UGG, serves as the determinant for MazF cleavage. Notably, statistical analysis predicted that two transcripts, which are unique in the autotroph, comprise the prime targets of the MazF endoribonuclease: hydroxylamine dehydrogenase (hao), which is essential for ammonia oxidation, and a large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL), which plays an important role in carbon assimilation. Given that N. europaea obtains energy and reductants via ammonia oxidation and the carbon for its growth from carbon dioxide, the chemolithotroph might use the MazF endoribonuclease to modulate its translation profile and subsequent biochemical reactions.
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Affiliation(s)
- Tatsuki Miyamoto
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Yuri Ota
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Masako Tsuruga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Rie Aoi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
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9
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Quorum Sensing Extracellular Death Peptides Enhance the Endoribonucleolytic Activities of Mycobacterium tuberculosis MazF Toxins. mBio 2018; 9:mBio.00685-18. [PMID: 29717013 PMCID: PMC5930309 DOI: 10.1128/mbio.00685-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
mazEF is a toxin-antitoxin module located on chromosomes of most bacteria. MazF toxins are endoribonucleases antagonized by MazE antitoxins. Previously, we characterized several quorum sensing peptides called "extracellular death factors" (EDFs). When secreted from bacterial cultures, EDFs induce interspecies cell death. EDFs also enhance the endoribonucleolytic activity of Escherichia coli MazF. Mycobacterium tuberculosis carries several mazEF modules. Among them, the endoribonucleolytic activities of MazF proteins mt-1, mt-3, and mt-6 were identified. MazF-mt6 and MazF-mt-3 cleave M. tuberculosis rRNAs. Here we report the in vitro effects of EDFs on the endoribonucleolytic activities of M. tuberculosis MazFs. Escherichia coli EDF (EcEDF) and the three Pseudomonas aeruginosa EDFs (PaEDFs) individually enhance the endoribonucleolytic activities of MazF-mt6 and MazF-mt3 and overcome the inhibitory effect of MazE-mt3 or MazE-mt6 on the endoribonucleolytic activities of the respective toxins. We propose that these EDFs can serve as a basis for a novel class of antibiotics against M. tuberculosis. Mycobacterium tuberculosis is one of the leading causes of death from infectious disease. M. tuberculosis is highly drug resistant, and drug delivery to the infected site is very difficult. In previous studies, we showed that extracellular death factors (EDFs) can work as quorum sensing molecules which participate in interspecies bacterial cell death. In this study, we demonstrated the role of different EDFs in the endoribonucleolytic activities of M. tuberculosis MazFs. Escherichia coli EDF (EcEDF) and the three Pseudomonas aeruginosa EDFs (PaEDFs) individually enhance the endoribonucleolytic activities of MazF-mt6 and MazF-mt3. The current report provides a basis for the use of the EDF peptides EcEDF and PaEDF as novel antibiotics against M. tuberculosis.
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10
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Ahn DH, Lee KY, Lee SJ, Park SJ, Yoon HJ, Kim SJ, Lee BJ. Structural analyses of the MazEF4 toxin-antitoxin pair in Mycobacterium tuberculosis provide evidence for a unique extracellular death factor. J Biol Chem 2017; 292:18832-18847. [PMID: 28972145 DOI: 10.1074/jbc.m117.807974] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/20/2017] [Indexed: 11/06/2022] Open
Abstract
The bacterial toxin-antitoxin MazEF system in the tuberculosis (TB)-causing bacterium Mycobacterium tuberculosis is activated under unfavorable conditions, including starvation, antibiotic exposure, and oxidative stress. This system contains the ribonucleolytic enzyme MazF and has emerged as a promising drug target for TB treatments targeting the latent stage of M. tuberculosis infection and reportedly mediates a cell death process via a peptide called extracellular death factor (EDF). Although it is well established that the increase in EDF-mediated toxicity of MazF drives a cell-killing phenomenon, the molecular details are poorly understood. Moreover, the divergence in sequences among reported EDFs suggests that each bacterial species has a unique EDF. To address these open questions, we report here the structures of MazF4 and MazEF4 complexes from M. tuberculosis, representing the first MazEF structures from this organism. We found that MazF4 possesses a negatively charged MazE4-binding pocket in contrast to the positively charged MazE-binding pockets in homologous MazEF complex structures from other bacteria. Moreover, using NMR spectroscopy and biochemical assays, we unraveled the molecular interactions of MazF4 with its RNA substrate and with a new EDF homolog originating from M. tuberculosis The EDF homolog discovered here possesses a positively charged residue at the C terminus, making this EDF distinct from previously reported EDFs. Overall, our results suggest that M. tuberculosis evolved a unique MazF and EDF and that the distinctive EDF sequence could serve as a starting point for designing new anti-tuberculosis drugs. We therefore conclude that this study might contribute to the development of a new line of anti-tuberculosis agents.
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Affiliation(s)
- Do-Hwan Ahn
- From the Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742
| | - Ki-Young Lee
- From the Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742
| | - Sang Jae Lee
- From the Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742
| | - Sung Jean Park
- the College of Pharmacy, Gachon University, 534-2 Yeonsu-dong, Yeonsu-gu, Incheon
| | - Hye-Jin Yoon
- the Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, and
| | - Soon-Jong Kim
- the Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Bong-Jin Lee
- From the Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742,
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11
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Miyamoto T, Ota Y, Yokota A, Suyama T, Tsuneda S, Noda N. Characterization of a Deinococcus radiodurans MazF: A UACA-specific RNA endoribonuclease. Microbiologyopen 2017; 6. [PMID: 28675659 PMCID: PMC5635168 DOI: 10.1002/mbo3.501] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 04/20/2017] [Accepted: 05/03/2017] [Indexed: 11/15/2022] Open
Abstract
Microbes are known to withstand environmental stresses by using chromosomal toxin–antitoxin systems. MazEF is one of the most extensively studied toxin–antitoxin systems. In stressful environments, MazF toxins modulate translation by cleaving single‐stranded RNAs in a sequence‐specific fashion. Previously, a chromosomal gene located at DR0417 in Deinococcus radiodurans was predicted to code for a MazF endoribonuclease (MazFDR0417); however, its function remains unclear. In the present study, we characterized the molecular function of MazFDR0417. Analysis of MazFDR0417‐cleaved RNA sites using modified massively parallel sequencing revealed a unique 4‐nt motif, UACA, as a potential cleavage pattern. The activity of MazFDR0417 was also assessed in a real‐time fluorometric assay, which revealed that MazFDR0417 strictly recognizes the unique tetrad UACA. This sequence specificity may allow D. radiodurans to alter its translation profile and survive under stressful conditions.
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Affiliation(s)
- Tatsuki Miyamoto
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Yuri Ota
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Tetsushi Suyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
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12
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Tsang J. Bacterial plasmid addiction systems and their implications for antibiotic drug development. POSTDOC JOURNAL : A JOURNAL OF POSTDOCTORAL RESEARCH AND POSTDOCTORAL AFFAIRS 2017; 5:3-9. [PMID: 28781980 PMCID: PMC5542005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria frequently carry mobile genetic elements capable of being passed to other bacterial cells. An example of this is the transfer of plasmids (small, circular DNA molecules) that often contain antibiotic resistance genes from one bacterium to another. Plasmids have evolved mechanisms to ensure their survival through generations by employing plasmids segregation and replication machinery and plasmid addiction systems. Plasmid addiction systems utilize a post-segregational killing of cells that have not received a plasmid. In this review, the types of plasmid addiction systems are described as well as their prevalence in antibiotic resistant bacteria. Lastly, the possibility of targeting these plasmid addiction systems for the treatment of antibiotic resistant bacterial infections is explored.
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Affiliation(s)
- Jennifer Tsang
- Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
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13
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Imanishi M, Tsuji S, Suda A, Futaki S. Detection ofN6-methyladenosine based on the methyl-sensitivity of MazF RNA endonuclease. Chem Commun (Camb) 2017; 53:12930-12933. [DOI: 10.1039/c7cc07699a] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
MazF RNA endonuclease was found to be sensitive toN6-methyladenosine, permitting facile analyses of m6A regulatory enzyme activity.
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Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research
- Kyoto University
- Uji, Kyoto 611-0011
- Japan
| | - Shogo Tsuji
- Institute for Chemical Research
- Kyoto University
- Uji, Kyoto 611-0011
- Japan
| | - Akiyo Suda
- Institute for Chemical Research
- Kyoto University
- Uji, Kyoto 611-0011
- Japan
| | - Shiroh Futaki
- Institute for Chemical Research
- Kyoto University
- Uji, Kyoto 611-0011
- Japan
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14
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AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea. Toxins (Basel) 2016; 8:toxins8060174. [PMID: 27271670 PMCID: PMC4926141 DOI: 10.3390/toxins8060174] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/30/2016] [Indexed: 02/07/2023] Open
Abstract
Nitrosomonas europaea carries numerous toxin-antitoxin systems. However, despite the abundant representation in its chromosome, studies have not surveyed the underlying molecular functions in detail, and their biological roles remain enigmatic. In the present study, we found that a chromosomally-encoded MazF family member, predicted at the locus NE1181, is a functional toxin endoribonuclease, and constitutes a toxin-antitoxin system, together with its cognate antitoxin, MazE. Massive parallel sequencing provided strong evidence that this toxin endoribonuclease exhibits RNA cleavage activity, primarily against the AAU triplet. This sequence-specificity was supported by the results of fluorometric assays. Our results indicate that N. europaea alters the translation profile and regulates its growth using the MazF family of endoribonuclease under certain stressful conditions.
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15
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Miyamoto T, Kato Y, Sekiguchi Y, Tsuneda S, Noda N. Characterization of MazF-Mediated Sequence-Specific RNA Cleavage in Pseudomonas putida Using Massive Parallel Sequencing. PLoS One 2016; 11:e0149494. [PMID: 26885644 PMCID: PMC4757574 DOI: 10.1371/journal.pone.0149494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/02/2016] [Indexed: 11/18/2022] Open
Abstract
Under environmental stress, microbes are known to alter their translation patterns using sequence-specific endoribonucleases that we call RNA interferases. However, there has been limited insight regarding which RNAs are specifically cleaved by these RNA interferases, hence their physiological functions remain unknown. In the current study, we developed a novel method to effectively identify cleavage specificities with massive parallel sequencing. This approach uses artificially designed RNAs composed of diverse sequences, which do not form extensive secondary structures, and it correctly identified the cleavage sequence of a well-characterized Escherichia coli RNA interferase, MazF, as ACA. In addition, we also determined that an uncharacterized MazF homologue isolated from Pseudomonas putida specifically recognizes the unique triplet, UAC. Using a real-time fluorescence resonance energy transfer assay, the UAC triplet was further proved to be essential for cleavage in P. putida MazF. These results highlight an effective method to determine cleavage specificity of RNA interferases.
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Affiliation(s)
- Tatsuki Miyamoto
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yuka Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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16
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Schuster CF, Mechler L, Nolle N, Krismer B, Zelder ME, Götz F, Bertram R. The MazEF Toxin-Antitoxin System Alters the β-Lactam Susceptibility of Staphylococcus aureus. PLoS One 2015; 10:e0126118. [PMID: 25965381 PMCID: PMC4428803 DOI: 10.1371/journal.pone.0126118] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/30/2015] [Indexed: 12/21/2022] Open
Abstract
Toxin-antitoxin (TA) systems are genetic elements of prokaryotes which encode a stable toxin and an unstable antitoxin that can counteract toxicity. TA systems residing on plasmids are often involved in episomal maintenance whereas those on chromosomes can have multiple functions. The opportunistic pathogen Staphylococcus aureus possesses at least four different families of TA systems but their physiological roles are elusive. The chromosomal mazEF system encodes the RNase toxin MazF and the antitoxin MazE. In the light of ambiguity regarding the cleavage activity, we here verify that MazF specifically targets UACAU sequences in S. aureus in vivo. In a native strain background and under non-stress conditions, cleavage was observed in the absence or presence of mazE. Transcripts of spa (staphylococcal protein A) and rsbW (anti-σB factor) were cut, but translational reporter fusions indicated that protein levels of the encoded products were unaffected. Despite a comparable growth rate as the wild-type, an S. aureus mazEF deletion mutant was more susceptible to β-lactam antibiotics, which suggests that further genes, putatively involved in the antibiotic stress response or cell wall synthesis or turnover, are controlled by this TA system.
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Affiliation(s)
- Christopher F. Schuster
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Lukas Mechler
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Nicoletta Nolle
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Bernhard Krismer
- Cellular and Molecular Microbiology, IMIT, University of Tübingen, German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Marc-Eric Zelder
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Friedrich Götz
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
| | - Ralph Bertram
- Department of Microbial Genetics, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany
- * E-mail:
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17
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RETRACTED: ChpK and MazF of the toxin-antitoxin modules are involved in the virulence of Leptospira interrogans during infection. Microbes Infect 2014; 17:34-47. [PMID: 25461800 DOI: 10.1016/j.micinf.2014.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/27/2014] [Accepted: 10/29/2014] [Indexed: 11/20/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the request of the corresponding author and the editorial office of Microbes and Infection. An independent reviewer of the retraction request was also appointed given that one of the authors is the Editor-in- Chief.
For figure 1C, Lanes 1 and 2 appear to share some unexpected similarities, except for the bottom band, which also appear to be the band of interest.
Sections of Figure 2C appear similar to sections of Figure 5D of a paper that had already appeared in Molecular Microbiology, volume 83, issue 5 (2012) 1006-1023. https://doi.org/10.1111/j.1365-2958.2012.07985.x.
In figure 3A, Flow cytograms share identical/similar patterns highlighted in various colours. Peculiarly, some of these patterns can be seen as horizontal rotations of others along the axis that separates different quadrants. (ie red green & purple). Moreover, some quadrants appear to have very high densities of events that are suprisingly limited by quadrant gates (most noticeably quadrants B2 from the second column of panels.
Figure 5A-B it was found that there were duplicated bands were produced.
Figures 5C and 5D, it was found that bands across each individual gel appear identical.
One of the conditions of submission of a paper for publication is that authors declare explicitly that the paper has not been previously published and is not under consideration for publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a misuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process”.
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18
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Loris R, Garcia-Pino A. Disorder- and Dynamics-Based Regulatory Mechanisms in Toxin–Antitoxin Modules. Chem Rev 2014; 114:6933-47. [DOI: 10.1021/cr400656f] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Remy Loris
- Molecular
Recognition Unit, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural
Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Abel Garcia-Pino
- Molecular
Recognition Unit, Structural Biology Research Center, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural
Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
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19
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Tripathi A, Dewan PC, Siddique SA, Varadarajan R. MazF-induced growth inhibition and persister generation in Escherichia coli. J Biol Chem 2013; 289:4191-205. [PMID: 24375411 DOI: 10.1074/jbc.m113.510511] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Toxin-antitoxin systems are ubiquitous in nature and present on the chromosomes of both bacteria and archaea. MazEF is a type II toxin-antitoxin system present on the chromosome of Escherichia coli and other bacteria. Whether MazEF is involved in programmed cell death or reversible growth inhibition and bacterial persistence is a matter of debate. In the present work the role of MazF in bacterial physiology was studied by using an inactive, active-site mutant of MazF, E24A, to activate WT MazF expression from its own promoter. The ectopic expression of E24A MazF in a strain containing WT mazEF resulted in reversible growth arrest. Normal growth resumed on inhibiting the expression of E24A MazF. MazF-mediated growth arrest resulted in an increase in survival of bacterial cells during antibiotic stress. This was studied by activation of mazEF either by overexpression of an inactive, active-site mutant or pre-exposure to a sublethal dose of antibiotic. The MazF-mediated persistence phenotype was found to be independent of RecA and dependent on the presence of the ClpP and Lon proteases. This study confirms the role of MazEF in reversible growth inhibition and persistence.
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Affiliation(s)
- Arti Tripathi
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India and
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20
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Larson AS, Hergenrother PJ. Light activation of Staphylococcus aureus toxin YoeBSa1 reveals guanosine-specific endoribonuclease activity. Biochemistry 2013; 53:188-201. [PMID: 24279911 DOI: 10.1021/bi4008098] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Staphylococcus aureus chromosome harbors two homologues of the YefM-YoeB toxin-antitoxin (TA) system. The toxins YoeBSa1 and YoeBSa2 possess ribosome-dependent ribonuclease (RNase) activity in Escherichia coli. This activity is similar to that of the E. coli toxin YoeBEc, an enzyme that, in addition to ribosome-dependent RNase activity, possesses ribosome-independent RNase activity in vitro. To investigate whether YoeBSa1 is also a ribosome-independent RNase, we expressed YoeBSa1 using a novel strategy and characterized its in vitro RNase activity, sequence specificity, and kinetics. Y88 of YoeBSa1 was critical for in vitro activity and cell culture toxicity. This residue was mutated to o-nitrobenzyl tyrosine (ONBY) via unnatural amino acid mutagenesis. YoeBSa1-Y88ONBY could be expressed in the absence of the antitoxin YefMSa1 in E. coli. Photocaged YoeBSa1-Y88ONBY displayed UV light-dependent RNase activity toward free mRNA in vitro. The in vitro ribosome-independent RNase activity of YoeBSa1-Y88ONBY, YoeBSa1-Y88F, and YoeBSa1-Y88TAG was significantly reduced or abolished. In contrast to YoeBEc, which cleaves RNA at both adenosine and guanosine with a preference for adenosine, YoeBSa1 cleaved mRNA specifically at guanosine. Using this information, a fluorometric assay was developed and used to determine the kinetic parameters for ribosome-independent RNA cleavage by YoeBSa1.
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Affiliation(s)
- Amy S Larson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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21
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Hobbs JK, Jiao W, Easter AD, Parker EJ, Schipper LA, Arcus VL. Change in heat capacity for enzyme catalysis determines temperature dependence of enzyme catalyzed rates. ACS Chem Biol 2013; 8:2388-93. [PMID: 24015933 DOI: 10.1021/cb4005029] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The increase in enzymatic rates with temperature up to an optimum temperature (Topt) is widely attributed to classical Arrhenius behavior, with the decrease in enzymatic rates above Topt ascribed to protein denaturation and/or aggregation. This account persists despite many investigators noting that denaturation is insufficient to explain the decline in enzymatic rates above Topt. Here we show that it is the change in heat capacity associated with enzyme catalysis (ΔC(‡)p) and its effect on the temperature dependence of ΔG(‡) that determines the temperature dependence of enzyme activity. Through mutagenesis, we demonstrate that the Topt of an enzyme is correlated with ΔC(‡)p and that changes to ΔC(‡)p are sufficient to change Topt without affecting the catalytic rate. Furthermore, using X-ray crystallography and molecular dynamics simulations we reveal the molecular details underpinning these changes in ΔC(‡)p. The influence of ΔC(‡)p on enzymatic rates has implications for the temperature dependence of biological rates from enzymes to ecosystems.
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Affiliation(s)
- Joanne K. Hobbs
- Department
of Biological Sciences, Faculty of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
| | - Wanting Jiao
- Biomolecular
Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand
| | - Ashley D. Easter
- Department
of Biological Sciences, Faculty of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
| | - Emily J. Parker
- Biomolecular
Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand
| | - Louis A. Schipper
- Department
of Earth and Ocean Sciences, Faculty of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
| | - Vickery L. Arcus
- Department
of Biological Sciences, Faculty of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
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22
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van Rensburg JJ, Hergenrother PJ. Detection of endogenous MazF enzymatic activity in Staphylococcus aureus. Anal Biochem 2013; 443:81-7. [PMID: 23994560 DOI: 10.1016/j.ab.2013.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/16/2013] [Accepted: 08/18/2013] [Indexed: 10/26/2022]
Abstract
The mazEFSa toxin-antitoxin (TA) system is ubiquitous in clinical isolates of Staphylococcus aureus, yet its physiological role is unclear. MazFSa is a sequence-specific endoribonuclease that inhibits the growth of S. aureus and Escherichia coli on ectopic overexpression. MazFSa preferentially cleaves RNA at UACAU sites, which are overrepresented in genes encoding pathogenicity factors. The exploitation of the inherent toxicity of MazFSa by artificial toxin activation has been proposed as an antibacterial strategy; however, enzymatic activity of endogenous MazFSa has never been detected, and tools for such analyses are lacking. Here we detail methods for detection of the ribonuclease activity of MazFSa, including a continuous fluorometric assay and a gel-based cleavage assay. Importantly, these methods allowed for the first detection of endogenous MazFSa enzymatic activity in S. aureus lysate. These robust and sensitive assays provide a toolkit for the identification, analysis, and validation of stressors that induce MazF enzymatic activity and should assist in the discovery of artificial activators of the mazEFSa TA system.
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Affiliation(s)
- Julia J van Rensburg
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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23
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Abstract
Escherichia coli mazEF is a toxin-antitoxin stress-induced module mediating cell death. It requires the quorum-sensing signal (QS) “extracellular death factor” (EDF), the penta-peptide NNWNN (EcEDF), enhancing the endoribonucleolytic activity of E. coli toxin MazF. Here we discovered that E. coli mazEF-mediated cell death could be triggered by QS peptides from the supernatants (SN) of the Gram-positive bacterium Bacillus subtilis and the Gram-negative bacterium Pseudomonas aeruginosa. In the SN of B. subtilis, we found one EDF, the hexapeptide RGQQNE, called BsEDF. In the SN of P. aeruginosa, we found three EDFs: the nonapeptide INEQTVVTK, called PaEDF-1, and two hexadecapeptides, VEVSDDGSGGNTSLSQ, called PaEDF-2, and APKLSDGAAAGYVTKA, called PaEDF-3. When added to a diluted E. coli cultures, each of these peptides acted as an interspecies EDF that triggered mazEF-mediated death. Furthermore, though their sequences are very different, each of these EDFs amplified the endoribonucleolytic activity of E. coli MazF, probably by interacting with different sites on E. coli MazF. Finally, we suggest that EDFs may become the basis for a new class of antibiotics that trigger death from outside the bacterial cells. Bacteria communicate with one another via quorum-sensing signal (QS) molecules. QS provides a mechanism for bacteria to monitor each other’s presence and to modulate gene expression in response to population density. Previously, we added E. coli EDF (EcEDF), the peptide NNWNN, to this list of QS molecules. Here we extended the group of QS peptides to several additional different peptides. The new EDFs are produced by two other bacteria, Bacillus subtilis and Pseudomonas aeruginosa. Thus, in this study we established a “new family of EDFs.” This family provides the first example of quorum-sensing molecules participating in interspecies bacterial cell death. Furthermore, each of these peptides provides the basis of a new class of antibiotics triggering death by acting from outside the cell.
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24
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Boynton TO, McMurry JL, Shimkets LJ. Characterization of Myxococcus xanthus MazF and implications for a new point of regulation. Mol Microbiol 2013; 87:1267-76. [PMID: 23369184 DOI: 10.1111/mmi.12165] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2013] [Indexed: 11/30/2022]
Abstract
During development, Myxococcus xanthus cells undergo programmed cell death (PCD) whereby 80% of vegetative cells die. Previously, the MazF RNA interferase has been implicated in this role. Recently, it was shown that deletion of the mazF gene does not eliminate PCD in wild-type strain DK1622 as originally seen in DZF1. To clarify the role of MazF, recombinant enzyme was characterized using a highly sensitive assay in the presence and absence of the proposed antitoxin MrpC. In contrast to previous reports that MrpC inhibits MazF activity, the hydrolysis rate was enhanced in a concentration-dependent manner with MrpC or MrpC2, an N-terminally truncated form of MrpC. Furthermore, MazF transcripts were not detected until 6-8 h post-induction, suggesting an antitoxin is unnecessary earlier. Potential MazF targets were identified and their transcript levels were shown to decline in DK1622 while remaining steady in a mazF deletion strain. Elimination of the mazF hydrolysis site in the nla6 transcript resulted in overproduction of the mRNA. Thus, MazF negatively regulates specific transcripts. Additionally, we show that discrepancies in the developmental phenotypes caused by removal of mazF in DK1622 and DZF1 are due to the presence of the pilQ1 allele in the latter strain.
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Affiliation(s)
- Tye O Boynton
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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25
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McKenzie JL, Duyvestyn JM, Smith T, Bendak K, MacKay J, Cursons R, Cook GM, Arcus VL. Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry. RNA (NEW YORK, N.Y.) 2012; 18:1267-1278. [PMID: 22539524 PMCID: PMC3358648 DOI: 10.1261/rna.031229.111] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 02/26/2012] [Indexed: 05/31/2023]
Abstract
The VapBC toxin-antitoxin (TA) family is the largest of nine identified TA families. The toxin, VapC, is a metal-dependent ribonuclease that is inhibited by its cognate antitoxin, VapB. Although the VapBCs are the largest TA family, little is known about their biological roles. Here we describe a new general method for the overexpression and purification of toxic VapC proteins and subsequent determination of their RNase sequence-specificity. Functional VapC was isolated by expression of the nontoxic VapBC complex, followed by removal of the labile antitoxin (VapB) using limited trypsin digestion. We have then developed a sensitive and robust method for determining VapC ribonuclease sequence-specificity. This technique employs the use of Pentaprobes as substrates for VapC. These are RNA sequences encoding every combination of five bases. We combine the RNase reaction with MALDI-TOF MS to detect and analyze the cleavage products and thus determine the RNA cut sites. Successful MALDI-TOF MS analysis of RNA fragments is acutely dependent on sample preparation methods. The sequence-specificity of four VapC proteins from two different organisms (VapC(PAE0151) and VapC(PAE2754) from Pyrobaculum aerophilum, and VapC(Rv0065) and VapC(Rv0617) from Mycobacterium tuberculosis) was successfully determined using the described strategy. This rapid and sensitive method can be applied to determine the sequence-specificity of VapC ribonucleases along with other RNA interferases (such as MazF) from a range of organisms.
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Affiliation(s)
| | | | - Tony Smith
- Department of Computer Science, University of Waikato, Hamilton 3240, New Zealand
| | - Katerina Bendak
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | - Joel MacKay
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
| | | | - Gregory M. Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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26
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Williams JJ, Hergenrother PJ. Artificial activation of toxin-antitoxin systems as an antibacterial strategy. Trends Microbiol 2012; 20:291-8. [PMID: 22445361 DOI: 10.1016/j.tim.2012.02.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/31/2012] [Accepted: 02/13/2012] [Indexed: 11/18/2022]
Abstract
Toxin-antitoxin (TA) systems are unique modules that effect plasmid stabilization via post-segregational killing of the bacterial host. The genes encoding TA systems also exist on bacterial chromosomes, and it has been speculated that these are involved in a variety of cellular processes. Interest in TA systems has increased dramatically over the past 5 years as the ubiquitous nature of TA genes on bacterial genomes has been revealed. The exploitation of TA systems as an antibacterial strategy via artificial activation of the toxin has been proposed and has considerable potential; however, efforts in this area remain in the early stages and several major questions remain. This review investigates the tractability of targeting TA systems to kill bacteria, including fundamental requirements for success, recent advances, and challenges associated with artificial toxin activation.
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Affiliation(s)
- Julia J Williams
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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27
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The Escherichia coli Extracellular Death Factor EDF Induces the Endoribonucleolytic Activities of the Toxins MazF and ChpBK. Mol Cell 2011; 41:625-35. [DOI: 10.1016/j.molcel.2011.02.023] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 10/17/2010] [Accepted: 12/24/2010] [Indexed: 01/15/2023]
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28
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Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R. PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure, and function. J Biol Chem 2009; 285:7254-70. [PMID: 20022964 DOI: 10.1074/jbc.m109.073387] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus anthracis genome harbors a toxin-antitoxin (TA) module encoding pemI (antitoxin) and pemK (toxin). This study describes the rPemK as a potent ribonuclease with a preference for pyrimidines (C/U), which is consistent with our previous study that demonstrated it as a translational attenuator. The in silico structural modeling of the PemK in conjunction with the site-directed mutagenesis confirmed the role of His-59 and Glu-78 as an acid-base couple in mediating the ribonuclease activity. The rPemK is shown to form a complex with the rPemI, which is in line with its function as a TA module. This rPemI-rPemK complex becomes catalytically inactive when both the proteins interact in a molar stoichiometry of 1. The rPemI displays vulnerability to proteolysis but attains conformational stability only upon rPemK interaction. The pemI-pemK transcript is shown to be up-regulated upon stress induction with a concomitant increase in the amount of PemK and a decline in the PemI levels, establishing the role of these modules in stress. The artificial perturbation of TA interaction could unleash the toxin, executing bacterial cell death. Toward this end, synthetic peptides are designed to disrupt the TA interaction. The peptides are shown to be effective in abrogating TA interaction in micromolar range in vitro. This approach can be harnessed as a potential antibacterial strategy against anthrax in the future.
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Affiliation(s)
- Shivangi Agarwal
- Laboratory of Molecular Biology and Genetic Engineering, , School of Biotechnology, Jawaharlal Nehru University, New Delhi-110067, India
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29
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Chan LL, Pineda M, Heeres JT, Hergenrother PJ, Cunningham BT. A general method for discovering inhibitors of protein-DNA interactions using photonic crystal biosensors. ACS Chem Biol 2008; 3:437-48. [PMID: 18582039 DOI: 10.1021/cb800057j] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Protein-DNA interactions are essential for fundamental cellular processes such as transcription, DNA damage repair, and apoptosis. As such, small molecule disruptors of these interactions could be powerful tools for investigation of these biological processes, and such compounds would have great potential as therapeutics. Unfortunately, there are few methods available for the rapid identification of compounds that disrupt protein-DNA interactions. Here we show that photonic crystal (PC) technology can be utilized to detect protein-DNA interactions, and can be used in a high-throughput screening mode to identify compounds that prevent protein-DNA binding. The PC technology is used to detect binding between protein-DNA interactions that are DNA-sequence-dependent (the bacterial toxin-antitoxin system MazEF) and those that are DNA-sequence-independent (the human apoptosis inducing factor (AIF)). The PC technology was further utilized in a screen for inhibitors of the AIF-DNA interaction, and through this screen aurin tricarboxylic acid was identified as the first in vitro inhibitor of AIF. The generality and simplicity of the photonic crystal method should enable this technology to find broad utility for identification of compounds that inhibit protein-DNA binding.
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Affiliation(s)
- Leo L. Chan
- Department of Electrical and Computer Engineering
| | | | | | - Paul J. Hergenrother
- Department of Biochemistry
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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Williams JJ, Hergenrother PJ. Exposing plasmids as the Achilles' heel of drug-resistant bacteria. Curr Opin Chem Biol 2008; 12:389-99. [PMID: 18625335 DOI: 10.1016/j.cbpa.2008.06.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2008] [Revised: 06/10/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
Abstract
Many multidrug-resistant bacterial pathogens harbor large plasmids that encode proteins conferring resistance to antibiotics. Although the acquisition of these plasmids often enables bacteria to survive in the presence of antibiotics, it is possible that plasmids also represent a vulnerability that can be exploited in tailored antibacterial therapy. This review highlights three recently described strategies designed to specifically combat bacteria harboring such plasmids: inhibition of plasmid conjugation, inhibition of plasmid replication, and exploitation of plasmid-encoded toxin-antitoxin systems.
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Affiliation(s)
- Julia J Williams
- Department of Microbiology, Roger Adams Laboratory, University of Illinois, Urbana, IL 61801, USA
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