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Hu X, Zhang X, Sun W, Liu C, Deng P, Cao Y, Zhang C, Xu N, Zhang T, Zhang Y, Liu JJ, Wang H. Systematic discovery of DNA-binding tandem repeat proteins. Nucleic Acids Res 2024; 52:10464-10489. [PMID: 39189466 PMCID: PMC11417379 DOI: 10.1093/nar/gkae710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024] Open
Abstract
Tandem repeat proteins (TRPs) are widely distributed and bind to a wide variety of ligands. DNA-binding TRPs such as zinc finger (ZNF) and transcription activator-like effector (TALE) play important roles in biology and biotechnology. In this study, we first conducted an extensive analysis of TRPs in public databases, and found that the enormous diversity of TRPs is largely unexplored. We then focused our efforts on identifying novel TRPs possessing DNA-binding capabilities. We established a protein language model for DNA-binding protein prediction (PLM-DBPPred), and predicted a large number of DNA-binding TRPs. A subset was then selected for experimental screening, leading to the identification of 11 novel DNA-binding TRPs, with six showing sequence specificity. Notably, members of the STAR (Short TALE-like Repeat proteins) family can be programmed to target specific 9 bp DNA sequences with high affinity. Leveraging this property, we generated artificial transcription factors using reprogrammed STAR proteins and achieved targeted activation of endogenous gene sets. Furthermore, the members of novel families such as MOON (Marine Organism-Originated DNA binding protein) and pTERF (prokaryotic mTERF-like protein) exhibit unique features and distinct DNA-binding characteristics, revealing interesting biological clues. Our study expands the diversity of DNA-binding TRPs, and demonstrates that a systematic approach greatly enhances the discovery of new biological insights and tools.
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Affiliation(s)
- Xiaoxuan Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuechun Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Sun
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chunhong Liu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Pujuan Deng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuanwei Cao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenze Zhang
- National Key Laboratory of Efficacy and Mechanism on Chinese Medicine for Metabolic Diseases, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ning Xu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongtong Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun-Jie Gogo Liu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
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Goodson JR, Zhang C, Trettel D, Ailinger HE, Lee PE, Spirito CM, Winkler WC. An autoinhibitory mechanism controls RNA-binding activity of the nitrate-sensing protein NasR. Mol Microbiol 2020; 114:348-360. [PMID: 32314426 PMCID: PMC7496416 DOI: 10.1111/mmi.14517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
Abstract
The ANTAR domain harnesses RNA‐binding activity to promote transcription attenuation. Although several ANTAR proteins have been analyzed by high‐resolution structural analyses, the residues involved in RNA‐recognition and transcription attenuation have not been identified. Nor is it clear how signal‐responsive domains are allosterically coupled with ANTAR domains for control of gene expression. Herein, we examined the sequence conservation of ANTAR domains to find residues that may associate with RNA. We subjected the corresponding positions of Klebsiella oxytoca NasR to site‐directed alanine substitutions and measured RNA‐binding activity. This revealed a functionally important patch of residues that forms amino acid pairing interactions with residues from NasR’s nitrate‐sensing NIT domain. We hypothesize these amino acid pairing interactions are part of an autoinhibitory mechanism that holds the structure in an “off” state in the absence of nitrate signal. Indeed, mutational disruption of these interactions resulted in constitutively active proteins, freed from autoinhibition and no longer influenced by nitrate. Moreover, sequence analyses suggested the autoinhibitory mechanism has been evolutionarily maintained by NasR proteins. These data reveal a molecular mechanism for how NasR couples its nitrate signal to RNA‐binding activity, and generally show how signal‐responsive domains of one‐component regulatory proteins have evolved to exert control over RNA‐binding ANTAR domains.
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Affiliation(s)
- Jonathan R Goodson
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Christopher Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Daniel Trettel
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD, USA
| | - Heather E Ailinger
- FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
| | - Priscilla E Lee
- FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
| | - Catherine M Spirito
- FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA.,Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD, USA.,FIRE: The First-Year Innovation & Research Experience Program, The University of Maryland, College Park, MD, USA
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Davydova A, Krasitskaya V, Vorobjev P, Timoshenko V, Tupikin A, Kabilov M, Frank L, Venyaminova A, Vorobyeva M. Reporter-recruiting bifunctional aptasensor for bioluminescent analytical assays. RSC Adv 2020; 10:32393-32399. [PMID: 35516485 PMCID: PMC9056652 DOI: 10.1039/d0ra05117a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/21/2020] [Indexed: 12/26/2022] Open
Abstract
A novel structure-switching bioluminescent 2′-F-RNA aptasensor consists of analyte-binding and obelin-recruiting modules, joined into a bi-specific aptamer construct.
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Affiliation(s)
- Anna Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Vasilisa Krasitskaya
- Institute of Biophysics SB RAS
- Federal Research Center “Krasnoyarsk Science Center SB RAS”
- Krasnoyarsk 660036
- Russia
| | - Pavel Vorobjev
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
| | - Valentina Timoshenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Ludmila Frank
- Institute of Biophysics SB RAS
- Federal Research Center “Krasnoyarsk Science Center SB RAS”
- Krasnoyarsk 660036
- Russia
- Siberian Federal University
| | - Alya Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
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Development and characterization of novel 2'-F-RNA aptamers specific to human total and glycated hemoglobins. Anal Biochem 2019; 570:43-50. [PMID: 30742800 DOI: 10.1016/j.ab.2019.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 02/07/2023]
Abstract
Aptamers are short DNA and RNA fragments which bind their molecular targets with affinity and specificity comparable to those of antibodies. Here, we describe the selection of novel 2'-F-RNA aptamers against total human hemoglobin or its glycated form HbA1c. After SELEX and high-throughput sequencing of the enriched libraries, affinities and specificities of candidate aptamers and their truncated variants were examined by the solid-phase bioluminescent assay. As a result, we identified aptamers specific to both hemoglobins or only glycated HbA1c. The developed 2'-F-RNA aptamers have shown their applicability for detection of total and glycated hemoglobin in one sample.
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Tang XL, Zhou YX, Wu SM, Pan Q, Xia B, Zhang XL. CFP10 and ESAT6 aptamers as effective Mycobacterial antigen diagnostic reagents. J Infect 2014; 69:569-80. [PMID: 24968239 DOI: 10.1016/j.jinf.2014.05.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/21/2014] [Accepted: 05/09/2014] [Indexed: 01/12/2023]
Abstract
The development of effective Mycobacterial antigen diagnostic reagents remains a high priority. The 6-kDa early secreted antigenic target (ESAT6) and 10-kDa culture filtrate protein (CFP10) are secreted early by virulent Mycobacterium tuberculosis (M. tb) and are not present in the non-virulent Bacillus Calmette-Guerin (BCG). In this study, we used a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technique to screen for a functional ssDNA aptamer "antibody" that specifically bound to ESAT6-CFP10 (CE) protein. The selected single ssDNA aptamers (CE24 and CE15) demonstrated the highest specificity and binding affinity to CFP10 (CE24: Kd = 3.75 × 10(-7) M) and ESAT6 (CE15: Kd = 1.6 × 10(-7) M). We further detected CFP10 and ESAT6 proteins in serum samples from active pulmonary tuberculosis (TB) patients, extrapulmonary TB patients and healthy donors by using an enzyme-linked oligonucleotide assay (ELONA). The results showed that the sensitivity and specificity were 100% and 94.1% (using CE24 aptamer-based ELONA) and 89.6% and 94.1% (using CE15 aptamer-based ELONA), respectively. A good correlation was observed between aptamer-based ELONA and T-SPOT TB assay. Thus, our study suggests that CE24 and CE15 have potentially broad applications as early antigen diagnostic agents not only for active pulmonary TB, extrapulmonary TB, but also possibly for latent TB infection and TB with immune-deficiency.
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Affiliation(s)
- Xiao-Lei Tang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Donghu Road 165#, Wuhan 430071, Hubei Province, China
| | - Ya-Xiong Zhou
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Donghu Road 165#, Wuhan 430071, Hubei Province, China
| | - Si-Min Wu
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Donghu Road 165#, Wuhan 430071, Hubei Province, China; Department of Laboratory Medicine, Wuhan Medical Treatment Center, Wuhan, China
| | - Qin Pan
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Donghu Road 165#, Wuhan 430071, Hubei Province, China
| | - Bing Xia
- Department of Gastroenterology and Research of Digestive Diseases, Zhongnan Hospital, Wuhan University School of Medicine, Wuhan 430071, China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Basic Medical Sciences, Donghu Road 165#, Wuhan 430071, Hubei Province, China.
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Orso F, Corà D, Ubezio B, Provero P, Caselle M, Taverna D. Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes. BMC Genomics 2010; 11:355. [PMID: 20525283 PMCID: PMC2890567 DOI: 10.1186/1471-2164-11-355] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 06/03/2010] [Indexed: 12/20/2022] Open
Abstract
Background Different approaches have been developed to dissect the interplay between transcription factors (TFs) and their cis-acting sequences on DNA in order to identify TF target genes. Here we used a combination of computational and experimental approaches to identify novel direct targets of TFAP2A, a key TF for a variety of physiological and pathological cellular processes. Gene expression profiles of HeLa cells either silenced for TFAP2A by RNA interference or not were previously compared and a set of differentially expressed genes was revealed. Results The regulatory regions of 494 TFAP2A-modulated genes were analyzed for the presence of TFAP2A binding sites, employing the canonical TFAP2A Positional Weight Matrix (PWM) reported in Jaspar http://jaspar.genereg.net/. 264 genes containing at least 2 high score TFAP2A binding sites were identified, showing a central role in "Cellular Movement" and "Cellular Development". In an attempt to identify TFs that could cooperate with TFAP2A, a statistically significant enrichment for SP1 binding sites was found for TFAP2A-activated but not repressed genes. The direct binding of TFAP2A or SP1 to a random subset of TFAP2A-modulated genes was demonstrated by Chromatin ImmunoPrecipitation (ChIP) assay and the TFAP2A-driven regulation of DCBLD2/ESDN/CLCP1 gene studied in details. Conclusions We proved that our computational approaches applied to microarray selected genes are valid tools to identify functional TF binding sites in gene regulatory regions as confirmed by experimental validations. In addition, we demonstrated a fine-tuned regulation of DCBLD2/ESDN transcription by TFAP2A.
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Affiliation(s)
- Francesca Orso
- Molecular Biotechnology Center (MBC), Department of Oncological Sciences, University of Torino, Torino, Italy
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