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Li T, Liu X, Qian H, Zhang S, Hou Y, Zhang Y, Luo G, Zhu X, Tao Y, Fan M, Wang H, Sha C, Lin A, Qin J, Gu K, Chen W, Fu T, Wang Y, Wei Y, Wu Q, Tan W. Blocker-SELEX: a structure-guided strategy for developing inhibitory aptamers disrupting undruggable transcription factor interactions. Nat Commun 2024; 15:6751. [PMID: 39117705 PMCID: PMC11310338 DOI: 10.1038/s41467-024-51197-w] [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: 01/11/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Despite the well-established significance of transcription factors (TFs) in pathogenesis, their utilization as pharmacological targets has been limited by the inherent challenges in modulating their protein interactions. The lack of defined small-molecule binding pockets and the nuclear localization of TFs do not favor the use of traditional tools. Aptamers possess large molecular weights, expansive blocking surfaces and efficient cellular internalization, making them compelling tools for modulating TF interactions. Here, we report a structure-guided design strategy called Blocker-SELEX to develop inhibitory aptamers (iAptamers) that selectively block TF interactions. Our approach leads to the discovery of iAptamers that cooperatively disrupt SCAF4/SCAF8-RNAP2 interactions, dysregulating RNAP2-dependent gene expression, which impairs cell proliferation. This approach is further applied to develop iAptamers blocking WDR5-MYC interactions. Overall, our study highlights the potential of iAptamers in disrupting pathogenic TF interactions, implicating their potential utility in studying the biological functions of TF interactions and in nucleic acids drug discovery.
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Affiliation(s)
- Tongqing Li
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Xueying Liu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Haifeng Qian
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Sheyu Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yu Hou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Yuchao Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Guoyan Luo
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Xun Zhu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Yanxin Tao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- Shanghai Institute of Material Medica, Chinese Academy of Sciences, Shanghai, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Mengyang Fan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Hong Wang
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Chulin Sha
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Ailan Lin
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Jingjing Qin
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Kedan Gu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Weichang Chen
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Ting Fu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Yajun Wang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Yong Wei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
| | - Qin Wu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Weihong Tan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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Zhu Y, Li X, Zhang Q, Yang X, Sun X, Pan Y, Yuan X, Ma Y, Xu B, Yang Z. Aptamer AS411 interacts with the KRAS promoter/hnRNP A1 complex and shows increased potency against drug-resistant lung cancer. RSC Med Chem 2024; 15:1515-1526. [PMID: 38784467 PMCID: PMC11110790 DOI: 10.1039/d3md00752a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 02/22/2024] [Indexed: 05/25/2024] Open
Abstract
G-quadruplex (G4) aptamers that can competitively binding protein with oncogene promoter G4 hold promise for cancer treatment. In this study, a neutral cytidinyl lipid, DNCA, was shown to transfect and deliver G4 aptamers (AS1411, TBA) into tumour cells, including multidrug-resistant tumour cells, and their nuclear localizations were clearly detected. Both AS1411/DNCA and TBA/DNCA showed excellent antitumour efficacies in the drug-resistant non-small cell lung cancer cell line A549/TXL at a low concentration (100 nM). Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was identified as a new target of AS1411 and TBA. The binding affinities were measured, and the Kd values of AS1411/hnRNP A1 and TBA/hnRNP A1 were 17.5 nM and 21.1 nM, respectively. Then the expression of KRAS mRNA in A549/TXL cells was found to be higher than that in A549 cells, and KRAS mRNA was reduced by approximately 40% after administration of AS1411 or TBA in A549/TXL cells. Further, it was confirmed for the first time that AS1411 targeted not only hnRNP A1 but also the KRAS promoter/hnRNP A1 complexes. And although TBA cannot target the KRAS promoter/hnRNP A1 complexes, the biolayer interferometry (BLI) experiment showed that TBA and AS1411 have similar effects on several key proteins in tumour cells, especially hnRNP A1. Molecular docking and molecular dynamics simulation showed that AS1411 and the KRAS promoter bound to the same domain of hnRNP A1 protein, while TBA bound to another domain.
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Affiliation(s)
- Yuejie Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Qi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
- School of Pharmacy, Chengdu Medical College 783 Xindu Avenue, Xindu District Chengdu 610500 China
| | - Xudong Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yi Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Bo Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
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Wang C, Yang J, Xu Z, Lv L, Chen S, Hong M, Liu JH. Promoter regulatory mode evolution enhances the high multidrug resistance of tmexCD1-toprJ1. mBio 2024; 15:e0021824. [PMID: 38564664 PMCID: PMC11077950 DOI: 10.1128/mbio.00218-24] [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: 01/24/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Antibiotic resistance could rapidly emerge from acquiring the mobile antibiotic resistance genes, which are commonly evolved from an intrinsic gene. The emergence of the plasmid-borne mobilized efflux pump gene cluster tmexCD1-toprJ1 renders the last-resort antibiotic tigecycline ineffective, although its evolutionary mechanism remains unclear. In this study, we investigate the regulatory mechanisms of the progenitor NfxB-MexCD-OprJ, a chromosomally encoded operon that does not mediate antibiotic resistance in the wild-type version, and its homologs, TNfxB1-TMexCD1-TOprJ1 mediating high-level tigecycline resistance, and TNfxB3-TMexCD3-TOprJ1. Mechanistic studies demonstrated that in nfxB-mexCD-oprJ, MexCD expression was under a weaker promoter, PmexC and inhibited by a strong repressor NfxB. For tmexCD1-toprJ1, TMexCD1 was highly expressed owing to the presence of a strong promoter, PtmexC1, and an inactive suppressor, TNfxB1, with a T39R mutation that rendered it unable to bind to promoter DNA. In tnfxB3-tmexCD3-toprJ1b, TMexCD3 expression was intermediate because of the local regulator TNfxB3, which binds to two inverted repeat sequences of PtmexC. Additionally, TNfxB3 exhibited lower protein expression and weaker DNA binding affinity than its ancestor NfxB, together with their promoter activities difference explaining the different expression levels of tmexCD-toprJ homologs. Distinct fitness burdens on these homologs-carrying bacteria were observed due to the corresponding expression level, which might be associated with their global prevalence. In summary, our data depict the mechanisms underlying the evolution and dissemination of an important mobile antibiotic resistance gene from an intrinsic chromosomal gene.IMPORTANCEAs antibiotic resistance seriously challenges global health, tigecycline is one of the few effective drugs in the pipeline against infections caused by multidrug-resistant pathogens. Our previous work identified a novel tigecycline resistance efflux pump gene cluster tmexCD1-toprJ1 in animals and humans, together with its various variants, a rising clinical concern. Herein, this study focused on how the local regulation modes of tmexCD1-toprJ1 evolved to a highly expressed efflux pump. Through comparative analysis between three tnfxB-tmexCD-toprJ homologs and their progenitor nfxB-mexCD-oprJ, modes, we demonstrated the evolutionary dynamics from a chromosomal silent gene to an active state. We found the de-repression of the local regulator and an increase of the promoter activity work together to promote a high production of drug efflux machines and enhance multidrug resistance. Our findings revealed that TMexCD1-TOprJ1 adopts a distinct evolutionary path to achieve higher multidrug resistance, urgently needing tight surveillance.
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Affiliation(s)
- Chengzhen Wang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Jun Yang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Luchao Lv
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
| | - Jian-Hua Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
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Zhu Y, Luo B, Mou X, Song Y, Zhou Y, Luo Y, Sun B, Luo Y, Tang H, Su Z, Bao R. Pseudomonas aeruginosa regulator PvrA binds simultaneously to multiple pseudo-palindromic sites for efficient transcription activation. SCIENCE CHINA. LIFE SCIENCES 2024; 67:900-912. [PMID: 37938507 DOI: 10.1007/s11427-022-2363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/10/2023] [Indexed: 11/09/2023]
Abstract
Tetracycline repressor (TetR) family regulators (TFRs) are the largest group of DNA-binding transcription factors and are widely distributed in bacteria and archaea. TFRs play vital roles in controlling the expression of various genes and regulating diverse physiological processes. Recently, a TFR protein Pseudomonas virulence regulator A (PvrA), was identified from Pseudomonas aeruginosa as the transcriptional activator of genes involved in fatty acid utilization and bacterial virulence. Here, we show that PvrA can simultaneously bind to multiple pseudo-palindromic sites and upregulate the expression levels of target genes. Cryo-electron microscopy (cryo-EM) analysis indicates the simultaneous DNA recognition mechanism of PvrA and suggests that the bound DNA fragments consist of a distorted B-DNA double helix. The crystal structure and functional analysis of PvrA reveal a hinge region that secures the correct domain motion for recognition of the promiscuous promoter. Additionally, our results showed that mutations disrupting the regulatory hinge region have differential effects on biofilm formation and pyocyanin biosynthesis, resulting in attenuated bacterial virulence. Collectively, these findings will improve the understanding of the relationship between the structure and function of the TetR family and provide new insights into the mechanism of regulation of P. aeruginosa virulence.
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Affiliation(s)
- Yibo Zhu
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Accurate Biotechnology (Hunan) Co., Ltd, Changsha, 410006, China
| | - Bingnan Luo
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xingyu Mou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yingjie Song
- College of Life Science, Sichuan Normal University, Chengdu, 610101, China
| | - Yonghong Zhou
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, 850000, China
| | - Yongbo Luo
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Youfu Luo
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hong Tang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhaoming Su
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Xiao Y, Qin T, He S, Chen Y, Li H, He Q, Wang X, Yang S. Systematic investigation of TetR-family transcriptional regulators and their roles on lignocellulosic inhibitor acetate tolerance in Zymomonas mobilis. Front Bioeng Biotechnol 2024; 12:1385519. [PMID: 38585710 PMCID: PMC10998469 DOI: 10.3389/fbioe.2024.1385519] [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: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
TetR-family transcriptional regulators are widely distributed among bacteria and involved in various cellular processes such as multidrug and inhibitor resistance. Zymomonas mobilis is a industrial bacterium for lignocellulosic ethanol production. Although TetR-family regulators and their associated RND-family efflux pumps in Z. mobilis have been identified to be differentially expressed under various inhibitors and stressful conditions, there are no systematic investigation yet. In this study, bioinformatic analyses indicated that there are three TetR-family transcriptional regulators (ZMO0281, ZMO0963, ZMO1547) and two RND-family efflux pumps (ZMO0282-0285, ZMO0964-0966) adjacent to corresponding TetR-family regulators of ZMO0281 and ZMO0963 in Z. mobilis. Genetics studies were then carried out with various mutants of TetR-family regulators constructed, and ZMO0281 was characterized to be related to acetate tolerance. Combining transcriptomics and dual-reporter gene system, this study demonstrated that three TetR-family regulators repressed their adjacent genes specifically. Moreover, TetR-family regulator ZMO0281 might also be involved in other cellular processes in the presence of acetate. In addition, the upregulation of RND-family efflux pumps due to ZMO0281 deletion might lead to an energy imbalance and decreased cell growth in Z. mobilis under acetate stress. The systematic investigation of all three TetR-family regulators and their roles on a major lignocellulosic inhibitor acetate tolerance in Z. mobilis thus not only unravels the molecular mechanisms of TetR-family regulators and their potential cross-talks on regulating RND-family efflux pumps and other genes in Z. mobilis, but also provides guidance on understanding the roles of multiple regulators of same family in Z. mobilis and other microorganisms for efficient lignocellulosic biochemical production.
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Affiliation(s)
- Yubei Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Tongjia Qin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
- Chinese Medicine College, Guangdong Yunfu Vocational College of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shuche He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Han Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Qiaoning He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Xia Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan, China
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He S, Taher NM, Hvorecny KL, Ragusa MJ, Bahl CD, Hickman AB, Dyda F, Madden DR. Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.572601. [PMID: 38293063 PMCID: PMC10827105 DOI: 10.1101/2024.01.16.572601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa infects cystic fibrosis (CF) patient airways and produces a virulence factor Cif that is associated with worse outcomes. Cif is an epoxide hydrolase that reduces cell-surface abundance of the cystic fibrosis transmembrane conductance regulator (CFTR) and sabotages pro-resolving signals. Its expression is regulated by a divergently transcribed TetR family transcriptional repressor. CifR represents the first reported epoxide-sensing bacterial transcriptional regulator, but neither its interaction with cognate operator sequences nor the mechanism of activation has been investigated. Using biochemical and structural approaches, we uncovered the molecular mechanisms controlling this complex virulence operon. We present here the first molecular structures of CifR alone and in complex with operator DNA, resolved in a single crystal lattice. Significant conformational changes between these two structures suggest how CifR regulates the expression of the virulence gene cif. Interactions between the N-terminal extension of CifR with the DNA minor groove of the operator play a significant role in the operator recognition of CifR. We also determined that cysteine residue Cys107 is critical for epoxide sensing and DNA release. These results offer new insights into the stereochemical regulation of an epoxide-based virulence circuit in a critically important clinical pathogen.
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Affiliation(s)
- Susu He
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Noor M. Taher
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Kelli L. Hvorecny
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Michael J. Ragusa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
- Department of Chemistry, Dartmouth, Hanover, NH 03755 USA
| | - Christopher D. Bahl
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Alison B. Hickman
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Fred Dyda
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Dean R. Madden
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
- Department of Chemistry, Dartmouth, Hanover, NH 03755 USA
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [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: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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Yu Y, Shao C, Gong X, Quan H, Liu D, Chen Q, Chu Y. Antimicrobial Resistance Surveillance of Tigecycline-Resistant Strains Isolated from Herbivores in Northwest China. Microorganisms 2022; 10:microorganisms10122432. [PMID: 36557685 PMCID: PMC9784582 DOI: 10.3390/microorganisms10122432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
There is no doubt that antimicrobial resistance (AMR) is a global threat to public health and safety, regardless of whether it’s caused by people or natural transmission. This study aimed to investigate the genetic characteristics and variations of tigecycline-resistant Gram-negative isolates from herbivores in northwest China. In this study, a total of 300 samples were collected from various provinces in northwest China, and 11 strains (3.67%) of tigecycline-resistant bacteria were obtained. In addition, bacterial identification and antibiotic susceptibility testing against 14 antibiotics were performed. All isolates were multiple drug-resistant (MDR) and resistant to more than three kinds of antibiotics. Using an Illumina MiSeq platform, 11 tigecycline-resistant isolates were sequenced using whole genome sequencing (WGS). The assembled draft genomes were annotated, and then sequences were blasted against the AMR gene database and virulence factor database. Several resistance genes mediating drug resistance were detected by WGS, including fluoroquinolone resistance genes (gyrA_S83L, gyrA_D87N, S83L, parC_S80I, and gyrB_S463A), fosfomycin resistance genes (GlpT_E448K and UhpT_E350Q), beta-lactam resistance genes (FtsI_D350N and S357N), and the tigecycline resistance gene (tetR N/A). Furthermore, there were five kinds of chromosomally encoded genetic systems that confer MDR (MarR_Y137H, G103S, MarR_N/A, SoxR_N/A, SoxS_N/A, AcrR N/A, and MexZ_K127E). A comprehensive analysis of MDR strains derived from WGS was used to detect variable antimicrobial resistance genes and their precise mechanisms of resistance. In addition, we found a novel ST type of Escherichia coli (ST13667) and a newly discovered point mutation (K127E) in the MexZ gene of Pseudomonas aeruginosa. WGS plays a crucial role in AMR control, prevention strategies, as well as multifaceted intervention strategies.
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Affiliation(s)
- Yongfeng Yu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Changchun Shao
- Lanzhou Institute for Food and Drug Control, Lanzhou 730050, China
| | - Xiaowei Gong
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Heng Quan
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Donghui Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Qiwei Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- Correspondence: (Q.C.); (Y.C.)
| | - Yuefeng Chu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- Correspondence: (Q.C.); (Y.C.)
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10
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Mahas A, Wang Q, Marsic T, Mahfouz MM. Development of Cas12a-Based Cell-Free Small-Molecule Biosensors via Allosteric Regulation of CRISPR Array Expression. Anal Chem 2022; 94:4617-4626. [PMID: 35266687 PMCID: PMC8943526 DOI: 10.1021/acs.analchem.1c04332] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Cell-free biosensors
can detect various molecules, thus promising
to transform the landscape of diagnostics. Here, we developed a simple,
rapid, sensitive, and field-deployable small-molecule detection platform
based on allosteric transcription factor (aTF)-regulated expression
of a clustered regularly interspaced short palindromic repeats (CRISPR)
array coupled to Cas12a activity. To this end, we engineered an expression
cassette harboring a T7 promoter, an aTF binding sequence, a Cas12a
CRISPR array, and protospacer adjacent motif-flanked Cas12a target
sequences. In the presence of the ligand, dissociation of the aTF
allows transcription of the CRISPR array; this leads to activation
of Cas12a collateral activity, which cleaves a single-stranded DNA
linker to free a quenched fluorophore, resulting in a rapid, significant
increase of fluorescence. As a proof of concept, we used TetR as the
aTF to detect different tetracycline antibiotics with high sensitivity
and specificity and a simple, hand-held visualizer to develop a fluorescence-based
visual readout. We also adapted a mobile phone application to further
simplify the interpretation of the results. Finally, we showed that
the reagents could be lyophilized to facilitate storage and distribution.
This detection platform represents a valuable addition to the toolbox
of cell-free, CRISPR-based biosensors, with great potential for in-field
deployment to detect non-nucleic acid small molecules.
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Affiliation(s)
- Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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11
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敬 美, 卢 淼, 郑 婷, 龚 涛, 李 雨, 周 学. [ frtR Gene Affects Acid Production and Demineralization Ability of Streptococcus mutans]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2022; 53:263-267. [PMID: 35332727 PMCID: PMC10409359 DOI: 10.12182/20220360104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 06/14/2023]
Abstract
Objective To study the effect of the frtR gene of TetR family on the acid production ability of Streptococcus mutans( S. mutans) and the bacteria's ability to induce tooth demineralization . Methods The growth of two strains of S. mutans UA159, Δ frtR, the frtR gene in-frame deletion strain, and Δ frtR/pDL278- frtR, the complement strain, was examined. The structure of biofilm was observed by laser scanning confocal microscopy (LSCM). The quantitative determination of water-insoluble extracellular polysaccharide (EPS) in the bacterial biofilms was done by anthrone-sulfuric acid method. The acid production capacity of S. mutans was measured by glycolytic pH drop. The demineralization-inducing ability of the strains on bovine teeth was determined by transverse microradiography (TMR). Results The growth curves of the strains showed that frtR did not affect the growth of S. mutans. According to the findings of LSCM observation, frtR did not affect the biofilm formation. According to the findings of the anthrone-sulfuric acid method, frtR did not have any significant impact on the EPS synthesis of S. mutans. The results of the glycolytic pH drop assay showed that the deletion of frtR delayed the rate of acid production by S. mutans when sucrose was the only carbon source. In addition, according to the TMR results, knocking out frtR reduced the depth and amount of demineralization induced by S. mutans on the surface of bovine teeth. Conclusion The deletion of frtR can weaken the acid production ability and the demineralization ability of S. mutans.
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Affiliation(s)
- 美玲 敬
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 淼 卢
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 婷 郑
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 涛 龚
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 雨庆 李
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 学东 周
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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12
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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13
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Kuťák D, Poppleton E, Miao H, Šulc P, Barišić I. Unified Nanotechnology Format: One Way to Store Them All. Molecules 2021; 27:63. [PMID: 35011301 PMCID: PMC8746876 DOI: 10.3390/molecules27010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.
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Affiliation(s)
- David Kuťák
- Business Unit Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
- Visualization Laboratory, Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic
| | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA; (E.P.); (P.Š.)
| | - Haichao Miao
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA; (E.P.); (P.Š.)
| | - Ivan Barišić
- Business Unit Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
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14
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Bertram R, Neumann B, Schuster CF. Status quo of tet regulation in bacteria. Microb Biotechnol 2021; 15:1101-1119. [PMID: 34713957 PMCID: PMC8966031 DOI: 10.1111/1751-7915.13926] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 11/27/2022] Open
Abstract
The tetracycline repressor (TetR) belongs to the most popular, versatile and efficient transcriptional regulators used in bacterial genetics. In the tetracycline (Tc) resistance determinant tet(B) of transposon Tn10, tetR regulates the expression of a divergently oriented tetA gene that encodes a Tc antiporter. These components of Tn10 and of other natural or synthetic origins have been used for tetracycline‐dependent gene regulation (tet regulation) in at least 40 bacterial genera. Tet regulation serves several purposes such as conditional complementation, depletion of essential genes, modulation of artificial genetic networks, protein overexpression or the control of gene expression within cell culture or animal infection models. Adaptations of the promoters employed have increased tet regulation efficiency and have made this system accessible to taxonomically distant bacteria. Variations of TetR, different effector molecules and mutated DNA binding sites have enabled new modes of gene expression control. This article provides a current overview of tet regulation in bacteria.
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Affiliation(s)
- Ralph Bertram
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Prof.-Ernst-Nathan-Straße 1, Nuremberg, 90419, Germany
| | - Bernd Neumann
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Prof.-Ernst-Nathan-Straße 1, Nuremberg, 90419, Germany
| | - Christopher F Schuster
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Burgstraße 37, Wernigerode, 38855, Germany
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15
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Dietler J, Schubert R, Krafft TGA, Meiler S, Kainrath S, Richter F, Schweimer K, Weyand M, Janovjak H, Möglich A. A Light-Oxygen-Voltage Receptor Integrates Light and Temperature. J Mol Biol 2021; 433:167107. [PMID: 34146595 DOI: 10.1016/j.jmb.2021.167107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Sensory photoreceptors enable organisms to adjust their physiology, behavior, and development in response to light, generally with spatiotemporal acuity and reversibility. These traits underlie the use of photoreceptors as genetically encoded actuators to alter by light the state and properties of heterologous organisms. Subsumed as optogenetics, pertinent approaches enable regulating diverse cellular processes, not least gene expression. Here, we controlled the widely used Tet repressor by coupling to light-oxygen-voltage (LOV) modules that either homodimerize or dissociate under blue light. Repression could thus be elevated or relieved, and consequently protein expression was modulated by light. Strikingly, the homodimeric RsLOV module from Rhodobacter sphaeroides not only dissociated under light but intrinsically reacted to temperature. The limited light responses of wild-type RsLOV at 37 °C were enhanced in two variants that exhibited closely similar photochemistry and structure. One variant improved the weak homodimerization affinity of 40 µM by two-fold and thus also bestowed light sensitivity on a receptor tyrosine kinase. Certain photoreceptors, exemplified by RsLOV, can evidently moonlight as temperature sensors which immediately bears on their application in optogenetics and biotechnology. Properly accounted for, the temperature sensitivity can be leveraged for the construction of signal-responsive cellular circuits.
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Affiliation(s)
- Julia Dietler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Roman Schubert
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Tobias G A Krafft
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Simone Meiler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Stephanie Kainrath
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Florian Richter
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Kristian Schweimer
- Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany
| | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany; Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany; Bayreuth Center for Biochemistry & Molecular Biology, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany.
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16
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Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
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Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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17
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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18
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Mol AA, Vogel M, Suess B. Inducible nuclear import by TetR aptamer-controlled 3' splice site selection. RNA (NEW YORK, N.Y.) 2021; 27:234-241. [PMID: 33148600 PMCID: PMC7812871 DOI: 10.1261/rna.077453.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Correct cellular localization is essential for the function of many eukaryotic proteins and hence cell physiology. Here, we present a synthetic genetic device that allows the control of nuclear and cytosolic localization based on controlled alternative splicing in human cells. The device is based on the fact that an alternative 3' splice site is located within a TetR aptamer that in turn is positioned between the branch point and the canonical splice site. The novel splice site is only recognized when the TetR repressor is bound. Addition of doxycycline prevents TetR aptamer binding and leads to recognition of the canonical 3' splice site. It is thus possible to produce two independent splice isoforms. Since the terminal loop of the aptamer may be replaced with any sequence of choice, one of the two isoforms may be extended by the respective sequence of choice depending on the presence of doxycycline. In a proof-of-concept study, we fused a nuclear localization sequence to a cytosolic target protein, thus directing the protein into the nucleus. However, the system is not limited to the control of nuclear localization. In principle, any target sequence can be integrated into the aptamer, allowing not only the production of a variety of different isoforms on demand, but also to study the function of mislocalized proteins. Moreover, it also provides a valuable tool for investigating the mechanism of alternative splicing in human cells.
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Affiliation(s)
- Adam A Mol
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
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19
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Ptacek J, Zhang D, Qiu L, Kruspe S, Motlova L, Kolenko P, Novakova Z, Shubham S, Havlinova B, Baranova P, Chen SJ, Zou X, Giangrande P, Barinka C. Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer. Nucleic Acids Res 2020; 48:11130-11145. [PMID: 32525981 PMCID: PMC7641732 DOI: 10.1093/nar/gkaa494] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 12/24/2022] Open
Abstract
Prostate-specific membrane antigen (PSMA) is a well-characterized tumor marker associated with prostate cancer and neovasculature of most solid tumors. PSMA-specific ligands are thus being developed to deliver imaging or therapeutic agents to cancer cells. Here, we report on a crystal structure of human PSMA in complex with A9g, a 43-bp PSMA-specific RNA aptamer, that was determined to the 2.2 Å resolution limit. The analysis of the PSMA/aptamer interface allows for identification of key interactions critical for nanomolar binding affinity and high selectivity of A9g for human PSMA. Combined with in silico modeling, site-directed mutagenesis, inhibition experiments and cell-based assays, the structure also provides an insight into structural changes of the aptamer and PSMA upon complex formation, mechanistic explanation for inhibition of the PSMA enzymatic activity by A9g as well as its ligand-selective competition with small molecules targeting the internal pocket of the enzyme. Additionally, comparison with published protein-RNA aptamer structures pointed toward more general features governing protein-aptamer interactions. Finally, our findings can be exploited for the structure-assisted design of future A9g-based derivatives with improved binding and stability characteristics.
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Affiliation(s)
- Jakub Ptacek
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Dong Zhang
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA
| | - Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA
| | - Sven Kruspe
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Lucia Motlova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Petr Kolenko
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic.,Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehova 7, Prague 11519, Czech Republic
| | - Zora Novakova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Shambhavi Shubham
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Barbora Havlinova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Petra Baranova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Shi-Jie Chen
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiaoqin Zou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Paloma Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Cyril Barinka
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
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