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Singh RN, Sani RK. Genome-Wide Computational Prediction and Analysis of Noncoding RNAs in Oleidesulfovibrio alaskensis G20. Microorganisms 2024; 12:960. [PMID: 38792789 PMCID: PMC11124144 DOI: 10.3390/microorganisms12050960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Noncoding RNAs (ncRNAs) play key roles in the regulation of important pathways, including cellular growth, stress management, signaling, and biofilm formation. Sulfate-reducing bacteria (SRB) contribute to huge economic losses causing microbial-induced corrosion through biofilms on metal surfaces. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation. This study aimed to identify ncRNAs in the genome of a model SRB, Oleidesulfovibrio alaskensis G20 (OA G20). Three in silico approaches revealed genome-wide distribution of 37 ncRNAs excluding tRNAs in the OA G20. These ncRNAs belonged to 18 different Rfam families. This study identified riboswitches, sRNAs, RNP, and SRP. The analysis revealed that these ncRNAs could play key roles in the regulation of several pathways of biosynthesis and transport involved in biofilm formation by OA G20. Three sRNAs, Pseudomonas P10, Hammerhead type II, and sX4, which were found in OA G20, are rare and their roles have not been determined in SRB. These results suggest that applying various computational methods could enrich the results and lead to the discovery of additional novel ncRNAs, which could lead to understanding the "rules of life of OA G20" during biofilm formation.
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Affiliation(s)
- Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD 57701, USA;
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD 57701, USA
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Zhang K, Wang K, Zhu X, Xie M, Xu F. A label-free kissing complex-induced fluorescence sensor for DNA and RNA detection by using DNA-templated silver nanoclusters as a signal transducer. RSC Adv 2016. [DOI: 10.1039/c6ra22515b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new strategy integrate silver nanoclusters (AgNCs) and riboswitches for the expanding of the application of a kissing complexes-induced sensor (KCIS) for the assay of DNA and RNA was reported.
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Affiliation(s)
- Kai Zhang
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Ke Wang
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Xue Zhu
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Minhao Xie
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Fei Xu
- Department of Laboratory Medicine
- Wuxi Municipal Women and Children Health Hospital
- Wuxi
- China
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3
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Matzner D, Mayer G. (Dis)similar Analogues of Riboswitch Metabolites as Antibacterial Lead Compounds. J Med Chem 2015; 58:3275-86. [PMID: 25603286 DOI: 10.1021/jm500868e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The rise of antimicrobial resistance in human pathogenic bacteria has increased the necessity for the discovery of novel, yet unexplored antibacterial drug targets. Riboswitches, which are embedded in untranslated regions of bacterial messenger RNA (mRNA), represent such an interesting target structure. These RNA elements regulate gene expression upon binding to natural metabolites, second messengers, and inorganic ions, such as fluoride with high affinity and in a highly discriminative manner. Recently, efforts have been directed toward the identification of artificial riboswitch activators by establishing high-throughput screening assays, fragment-based screening, and structure-guided ligand design approaches. Emphasis in this review is placed on the special requirements and synthesis of new potential antibiotic drugs that target riboswitches in which dissimilarity is an important aspect in the design of potential lead compounds.
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Affiliation(s)
- Daniel Matzner
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Huang W, Kim J, Jha S, Aboul-Ela F. Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine. J Mol Biol 2012; 418:331-49. [PMID: 22425639 DOI: 10.1016/j.jmb.2012.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/09/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
Abstract
Riboswitches are promising targets for the design of novel antibiotics and engineering of portable genetic regulatory elements. There is evidence that variability in riboswitch properties allows tuning of expression for genes involved in different stages of biosynthetic pathways by mechanisms that are not currently understood. Here, we explore the mechanism for tuning of S-adenosyl methionine (SAM)-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand SAM. SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine, SAM, and so forth. We use base-pair probability predictions to examine the secondary-structure folding landscape of several SAM-I riboswitch sequences. We predict different folding behaviors for different SAM-I riboswitch sequences. We identify several "decoy" base-pairing interactions involving 5' riboswitch residues that can compete with the formation of a P1 helix, a component of the ligand-bound "transcription OFF" state, in the absence of SAM. We hypothesize that blockage of these interactions through SAM contacts contributes to stabilization of the OFF state in the presence of ligand. We also probe folding patterns for a SAM-I riboswitch RNA using constructs with different 3' truncation points experimentally. Folding was monitored through fluorescence, susceptibility to base-catalyzed cleavage, nuclear magnetic resonance, and indirectly through SAM binding. We identify key decision windows at which SAM can affect the folding pathway towards the OFF state. The presence of decoy conformations and differential sensitivities to SAM at different transcript lengths is crucial for SAM-I riboswitches to modulate gene expression in the context of global cellular metabolism.
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Affiliation(s)
- Wei Huang
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA
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Roy M, Chakravarthi BVSK, Jayabaskaran C, Karande AA, Chakravarty AR. Impact of metal binding on the antitumor activity and cellular imaging of a metal chelator cationic imidazopyridine derivative. Dalton Trans 2011; 40:4855-64. [DOI: 10.1039/c0dt01717e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Water soluble cationic imidazopyridine species (1) having metal binding sites induces metal-assisted caspase dependent apoptosis in cancer cells and enhanced photodynamic effect in the presence of Fe2+or Zn2+ions.
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Affiliation(s)
- Mithun Roy
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 560 012
- India
| | | | | | - Anjali A. Karande
- Department of Biochemistry
- Indian Institute of Science
- Bangalore 560 012
- India
| | - Akhil R. Chakravarty
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 560 012
- India
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Abstract
Aptamers that target a specific cell subpopulation within composite mixtures represent invaluable tools in biomedical research and in the development of cell-specific therapeutics. Here we describe a detailed protocol for a modular and generally applicable scheme to select aptamers that target the subpopulations of cells in which you are interested. A fluorescence-activated cell-sorting device is used to simultaneously differentiate and separate those subpopulations of cells having bound and unbound aptamers. There are fewer false positives when using this approach in comparison with other cell-selection approaches in which unspecific binding of nucleic acids to cells with reduced membrane integrity or their unselective uptake by dead cells occurs more often. The protocol provides a state-of-the-art approach for identifying aptamers that selectively target virtually any cell type under investigation. As an example, we provide the step-by-step protocol targeting CD19(+) Burkitt's lymphoma cells, starting from the pre-SELEX (systematic evolution of ligands by exponential amplification) measurements to establish suitable SELEX conditions and ending at completion of the SELEX procedure, which reveals the enriched single-stranded DNA library.
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Lünse CE, Michlewski G, Hopp CS, Rentmeister A, Cáceres JF, Famulok M, Mayer G. An aptamer targeting the apical-loop domain modulates pri-miRNA processing. Angew Chem Int Ed Engl 2010; 49:4674-7. [PMID: 20533473 DOI: 10.1002/anie.200906919] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Christina E Lünse
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Strasse 1, Bonn, Germany
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Lünse C, Michlewski G, Hopp C, Rentmeister A, Cáceres J, Famulok M, Mayer G. Modulation der pri-miRNA-Reifung durch ein die apikale Schleife bindendes Aptamer. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Sasmal PK, Saha S, Majumdar R, De S, Dighe RR, Chakravarty AR. Oxovanadium(iv) complexes of phenanthroline bases: the dipyridophenazine complex as a near-IR photocytotoxic agent. Dalton Trans 2010; 39:2147-58. [DOI: 10.1039/b917265c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Affiliation(s)
- Michael Famulok
- LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Wieland M, Benz A, Klauser B, Hartig JS. Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew Chem Int Ed Engl 2009; 48:2715-8. [PMID: 19156802 DOI: 10.1002/anie.200805311] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNA Lego: The use of natural riboswitch aptamers in synthetic RNA switches (see picture) should broaden the scope of artificial RNA regulators dramatically. It is shown that thiamine pyrophosphate (TPP) aptamers can be used in engineered devices as very sensitive switches of gene expression in unmodified organisms. The approach demonstrates that intrinsic metabolites can be utilized as external effectors of cellular functions.
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Affiliation(s)
- Markus Wieland
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Wieland M, Benz A, Klauser B, Hartig J. Artificial Ribozyme Switches Containing Natural Riboswitch Aptamer Domains. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Roy M, Bhowmick T, Santhanagopal R, Ramakumar S, Chakravarty AR. Photo-induced double-strand DNA and site-specific protein cleavage activity of l-histidine (μ-oxo)diiron(iii) complexes of heterocyclic bases. Dalton Trans 2009:4671-82. [DOI: 10.1039/b901337g] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Roy M, Santhanagopal R, Chakravarty AR. DNA binding and oxidative DNA cleavage activity of (μ-oxo)diiron(iii) complexes in visible light. Dalton Trans 2009:1024-33. [DOI: 10.1039/b815215b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Abstract
RNA folds during transcription in the cell. Compared to most in vitro studies where the focus is generally on Mg(2+)-initiated refolding of fully synthesized transcripts, cotranscriptional RNA folding studies better replicate how RNA folds in a cellular environment. Unique aspects of cotranscriptional folding include the 5'- to 3'-polarity of RNA, the transcriptional speed, pausing properties of the RNA polymerase, the effect of the transcriptional complex and associated factors, and the effect of RNA-binding proteins. Identifying strategic pause sites can reveal insights on the folding pathway of the nascent transcript. Structural mapping of the paused transcription complexes identifies important folding intermediates along these pathways. Oligohybridization assays and the appearance of the catalytic activity of a ribozyme either in trans or in cis can be used to monitor cotranscriptional folding under a wide range of conditions. In our laboratory, these methodologies have been applied to study the folding of three highly conserved RNAs (RNase P, SRP, and tmRNA), several circularly permuted forms of a bacterial RNase P RNA, a riboswitch (thiM), and an aptamer-activated ribozyme (glmS).
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Affiliation(s)
- Terrence N Wong
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois, USA
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