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Duggal Y, Fontaine BM, Dailey DM, Ning G, Weinert EE. RNase I Modulates Escherichia coli Motility, Metabolism, and Resistance. ACS Chem Biol 2020; 15:1996-2004. [PMID: 32551492 DOI: 10.1021/acschembio.0c00390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria are constantly adapting to their environment by sensing extracellular factors that trigger production of intracellular signaling molecules, known as second messengers. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified in Escherichia coli and have emerged as possible novel signaling molecules. 2',3'-cNMPs are produced through endonucleolytic cleavage of short RNAs by the T2 endoribonuclease, RNase I; however, the physiological roles of RNase I remain unclear. Our transcriptomic analysis suggests that RNase I is involved in modulating numerous cellular processes, including nucleotide metabolism, motility, acid sensitivity, metal homeostasis, and outer membrane morphology. Through a combination of deletion strain and inhibitor studies, we demonstrate that RNase I plays a previously unknown role in E. coli stress resistance by affecting pathways that are part of the defense mechanisms employed by bacteria when introduced to external threats, including antibiotics. Thus, this work provides insight into the emerging roles of RNase I in bacterial signaling and physiology and highlights the potential of RNase I as a target for antibacterial adjuvants.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Benjamin M. Fontaine
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Deanna M. Dailey
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Gang Ning
- Microscopy Facility, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Santos-Cancel M, White RJ. Collagen Membranes with Ribonuclease Inhibitors for Long-Term Stability of Electrochemical Aptamer-Based Sensors Employing RNA. Anal Chem 2017; 89:5598-5604. [PMID: 28440619 PMCID: PMC5653965 DOI: 10.1021/acs.analchem.7b00766] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Electrochemical aptamer-based (E-AB) sensors offer advantageous analytical detection abilities due to their rapid response time (seconds to minutes), specificity to a target, and selectivity to function in complex media. Ribonucleic acid (RNA) aptamers employed in this class of sensor offer favorable binding characteristics resulting from the ability of RNA to form stable tertiary folds aided by long-range intermolecular interactions. As a result, RNA aptamers can fold into three-dimensional structures more complex than those of their DNA counterparts and consequently exhibit better binding ability to target analytes. Unfortunately, RNA aptamers are susceptible to degradation by nucleases, and for this reason, RNA-based sensors are scarce or require significant sample pretreatment before use in clinically relevant media. Here, we combine the usefulness of a collagen I hydrogel membrane with entrapped ribonuclease inhibitors (RI) to protect small molecule RNA E-AB sensors from endogenous nucleases in complex media. More specifically, the biocompatibility of the naturally polymerized hydrogel with encapsulated RI promotes the protection of an aminoglycoside-binding RNA E-AB sensor up to 6 h, enabling full sensor function in nuclease-rich environments (undiluted serum) without the need for prior sample preparation or oligonucleotide modification. The use of collagen as a biocompatible membrane represents a general approach to compatibly interface E-AB sensors with complex biological samples.
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Affiliation(s)
- Mirelis Santos-Cancel
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland 21250
| | - Ryan J. White
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland 21250
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Cisneros-Ruiz M, Mayolo-Deloisa K, Rito-Palomares M, Przybycien TM. Separation of PEGylated variants of ribonuclease A and apo-α-lactalbumin via reversed phase chromatography. J Chromatogr A 2014; 1360:209-16. [DOI: 10.1016/j.chroma.2014.07.085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/24/2014] [Accepted: 07/27/2014] [Indexed: 11/27/2022]
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4
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Tripathy DR, Dinda AK, Dasgupta S. A simple assay for the ribonuclease activity of ribonucleases in the presence of ethidium bromide. Anal Biochem 2013; 437:126-9. [PMID: 23499964 DOI: 10.1016/j.ab.2013.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 11/30/2022]
Abstract
The ribonuclease (RNase) activity of ribonucleases has been assayed by observing the change in fluorescence intensity of ethidium bromide on binding with yeast RNA. The binding of EtBr with RNA was monitored via UV-vis and fluorimetric methods. The degradation of RNA by RNase A was monitored by the change in fluorescence emission intensity of ethidium bromide at 600nm on excitation at 510nm. The ribonucleolytic activity of RNase A and angiogenin at various pH values was determined by this method. From this technique we have also determined the macroscopic pKa values of active site residues of these enzymes. This assay permits the evaluation of the catalytic efficiency of enzymatic proteins ranging from high ribonucleolytic activity to low ribonucleolytic activity toward the natural substrate RNA.
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Affiliation(s)
- Debi Ranjan Tripathy
- Department of Chemistry, Indian Institute of Technology, Kharagpur, Kharagpur 721302, India
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Abstract
Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).
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Affiliation(s)
- Nan Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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6
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Appel WPJ, Meijer EW, Dankers PYW. Enzymatic Activity at the Surface of Biomaterials via Supramolecular Anchoring of Peptides: The Effect of Material Processing. Macromol Biosci 2011; 11:1706-12. [DOI: 10.1002/mabi.201100225] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 07/25/2011] [Indexed: 12/15/2022]
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7
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Ye Y, Wen W, Xiang Y, Qi X, La Belle J, Chen J, Wang J. Direct Electrochemical Monitoring of RNase Activity. ELECTROANAL 2008. [DOI: 10.1002/elan.200804172] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Aumüller T, Fischer G. Bioactivity of Folding Intermediates Studied by the Recovery of Enzymatic Activity during Refolding. J Mol Biol 2008; 376:1478-92. [DOI: 10.1016/j.jmb.2007.12.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 12/17/2007] [Accepted: 12/21/2007] [Indexed: 10/22/2022]
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9
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Kanazawa M, Sato S, Ohtsuka K, Takenaka S. Ferrocenylnaphthalene diimide-based electrochemical ribonuclease assay. ANAL SCI 2008; 23:1415-9. [PMID: 18071228 DOI: 10.2116/analsci.23.1415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Messenger RNA (mRNA) poly(A)+RNA (from mouse kidney) was immobilized on a N-hydroxysuccinimide(NHS)-activated carboxylic acid modified electrode prepared by the treatment of a gold electrode with 3,3'-dithiodipropionic acid, followed by NHS and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). An electrochemical measurement using this mRNA electrode was carried out in an electrolyte containing ferrocenylnaphthalene diimide (1), and showed an electrochemical signal based on 1 concentrated on immobilized mRNA. After treating this electrode with water containing varied amounts of ribonuclease A (RNase A), the current peak based on 1 decreased with increasing in the amount of RNase A with a linear correlation in the range of 0.2-10 pg of RNase A.
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Affiliation(s)
- Masanori Kanazawa
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 840-8550, Japan
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Daly SM, Przybycien TM, Tilton RD. Adsorption of poly(ethylene glycol)-modified ribonuclease A to a poly(lactide-co-glycolide) surface. Biotechnol Bioeng 2005; 90:856-68. [PMID: 15841471 DOI: 10.1002/bit.20481] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein adsorption is a source of variability in the release profiles of therapeutic proteins from biodegradable microspheres. We employ optical reflectometry and total internal reflection fluorescence to explore the extent and kinetics of ribonuclease A (RNase A) adsorption to spin-cast films of poly(lactide-co-glycolide) (PLG) and, in particular, to determine how covalent grafting of polyethylene glycol (PEG) to RNase A affects adsorption. Adsorption kinetics on PLG surfaces are surface-limited for RNase A but transport-limited for unconjugated PEG homopolymers and for PEG-modified RNase A, indicating that PEG anchors the conjugates to the surface during the transport-limited regime. PEG modification of RNase A decreases the total number of adsorbed molecules per unit area but increases the areal surface coverage because the grafted PEG chains exclude additional surface area. Total internal reflection fluorescence-based exchange measurements show that there is no exchange between adsorbed and solution-phase protein molecules. This indicates an unusually tenacious adsorption. Streaming current measurements indicate that the zeta potential of the PLG surface becomes increasingly negative as the film is exposed to water for several weeks, as expected. Aging of the PLG surface results in increased adsorption of unmodified RNase A but decreased adsorption of unconjugated PEG homopolymers and of PEG-RNase A conjugates, relative to the extent of adsorption on freshly prepared PLG surfaces. Adsorption results correlate well with an increase in the rate, total extent and preservation of bioactivity of RNase A released from PLG microspheres for the PEG-modified version of RNase A.
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Affiliation(s)
- Susan M Daly
- Departments of Chemical Engineering and Biomedical Engineering, Center for Complex Fluids Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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Park C, Kelemen BR, Klink TA, Sweeney RY, Behlke MA, Eubanks SR, Raines RT. Fast, facile, hypersensitive assays for ribonucleolytic activity. Methods Enzymol 2002; 341:81-94. [PMID: 11582813 DOI: 10.1016/s0076-6879(01)41146-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- C Park
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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James DA, Burns DC, Woolley GA. Kinetic characterization of ribonuclease S mutants containing photoisomerizable phenylazophenylalanine residues. Protein Eng Des Sel 2001; 14:983-91. [PMID: 11809929 DOI: 10.1093/protein/14.12.983] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Incorporation of the photoisomerizable amino acid phenylazophenylalanine (PAP) into enzyme structures has been proposed as a strategy for photoswitching enzyme activity. To evaluate the strengths and limitations of this approach to enzyme photo-control, we performed a kinetic analysis of RNase S analogues containing PAP in positions 4, 7, 8, 10, 11 or 13. For an enzyme containing a single PAP group, the maximum extent of photoconversion (between approximately 96% trans/4% cis and 10% trans/90% cis under standard conditions) sets a limit on the maximum fold change in the initial rate of approximately 25-fold, if the cis form is the more active isomer, and approximately 10-fold if the trans form is more active. This extent of photoswitching was not realized in the present case because the effects of photoisomerization on kinetic constants were small and distributed among effects on S-peptide binding, substrate binding and the rate of the chemical step. These results suggest that photoisomerization could substantially alter enzyme kinetic constants but that a directed combinatorial approach might be required for realizing maximal photo-control in such systems. The limit set by the extent of photoconversion might be overcome by coupling multiple PAP groups to one enzyme or by altering the behaviour of a system that required oligomerization for activity.
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Affiliation(s)
- D A James
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, Canada, M5S 3H6
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Kelemen BR, Klink TA, Behlke MA, Eubanks SR, Leland PA, Raines RT. Hypersensitive substrate for ribonucleases. Nucleic Acids Res 1999; 27:3696-701. [PMID: 10471739 PMCID: PMC148625 DOI: 10.1093/nar/27.18.3696] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A substrate for a hypersensitive assay of ribonucleolytic activity was developed in a systematic manner. This substrate is based on the fluorescence quenching of fluorescein held in proximity to rhodamine by a single ribonucleotide embedded within a series of deoxynucleotides. When the substrate is cleaved, the fluorescence of fluorescein is manifested. The optimal substrate is a tetranucleotide with a 5',6-carboxyfluorescein label (6-FAM) and a 3',6-carboxy-tetramethylrhodamine (6-TAMRA) label: 6-FAM-dArUdAdA-6-TAMRA. The fluorescence of this substrate increases 180-fold upon cleavage. Bovine pancreatic ribonuclease A (RNase A) cleaves this substrate with a k (cat)/ K (m)of 3.6 x 10(7)M(-1)s(-1). Human angiogenin, which is a homolog of RNase A that promotes neovascularization, cleaves this substrate with a k (cat)/ K (m)of 3. 3 x 10(2)M(-1)s(-1). This value is >10-fold larger than that for other known substrates of angio-genin. With these attributes, 6-FAM-dArUdAdA-6-TAMRA is the most sensitive known substrate for detecting ribo-nucleolytic activity. This high sensitivity enables a simple protocol for the rapid determination of the inhibition constant ( K (i)) for competitive inhibitors such as uridine 3'-phosphate and adenosine 5'-diphos-phate.
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Affiliation(s)
- B R Kelemen
- Department of Biochemistry, University of Wisconsin-Madison, WI 53706, USA
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