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RNAse activity review

RNAse activity review


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I was searching for any review unravelling the structure-function motifs responsible for RNAse activity. Or at least a well-composed review of RNAse superfamilies that are described nowadays (with linkage to their functional activity). My PubMed search performed didn't give any valuable results for that. Any specialists to comment?

Thanks in advance!


I did a few searches, just for fun, but all I came up with was:

Yuhong Zuo and Murray P. Deutscher "Exoribonuclease superfamilies: structural analysis and phylogenetic distribution" (2001) Nucl. Acids Res. 29 (5): 1017-1026. doi: 10.1093/nar/29.5.1017

Not very recent, but it's open access. It might be possible to search for more recent papers that have cited this. Although I haven't tried it myself, I found suggestions for doing this at https://www.bc.edu/libraries/help/howdoi/howto/pubcitation.html.


Frontiers in Immunology

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    Immunity and Resistance to Viruses

    2′-5′ Oligo A Synthase Pathway

    Two ISGs are key to this pathway: ribonuclease L (RNaseL) and 2′-5′ oligo A synthase (OAS). RNaseL (for latent) is inactive when synthesized, but when activated destroys RNA within the cell, leading to autophagy and apoptosis. (Both of these processes are robust antiviral responses.) In order for RNAseL to become active, it must bind to polymers of 2′-5′-linked oligoadenylate (2′-5′ oligo A) and these are synthesized by OAS. However OAS is also produced in an inactive form and only becomes active upon binding to dsRNA. The requirement for a multistep pathway helps insure that RNaseL is not activated in the absence of viral infection. To summarize the pathway: (1) RNaseL and OAS are ISGs. (2) If a cell expressing these proteins is infected by an RNA virus, long dsRNA accumulates in the cytoplasm. (3) OAS is activated and synthesizes 2′-5′ oligo A. (4) RNaseL binds to 2′-5′oligo A and is activated. (5) Active RNaseL cleaves viral and cellular RNA.


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    Sodium acetate, trihydrate (Prod. No. S8625)
    Ribonucleic Acid (Prod. No. R6750)

    Use ultrapure water (≥18 MΩxcm resistivity at 25 °C) for the preparation of reagents.

    Buffer (100 mM Sodium Acetate, pH 5.0 at 25 °C) – Prepare a 13.61 mg/mL solution using Sodium acetate, trihydrate (Prod. No. S8625) in ultrapure water. Adjust pH to 5.0 at 25 °C with 2 M acetic acid.

    RNA Solution [0.1% (w/v) Ribonucleic Acid Solution] – Prepare

    1 mg/mL solution in Buffer using Ribonucleic Acid (Prod. No. R6750). Ensure dissolution by either swirling or inversion. Do not use a stir bar. Dissolution may take up to 30 minutes. Once the RNA has dissolved, the RNA concentration must be verified prior to running the assay. Pipette the following into 3.0 mL acrylate disposable cuvettes and mix by inversion:

    Determine the ΔA300 Substrate = A300 Substrate – A300 Blank. ΔA300 Substrate must be 0.73±0.025. If necessary, adjust the absorbance using appropriate amount of Buffer or solid Ribonucleic Acid.

    Enzyme Solution (RNase Solution) – Prepare a RNase Stock Solution containing 50–75 Kunitz units/mL in cold ultrapure water.

    • For Total Hydrolysis Determination (Ef) – Prepare a solution by diluting the RNase Stock Solution with cold ultrapure water to a final concentration of 0.50–0.75 Kunitz unit/mL.
    • For Rate Determination (E0) – Immediately before use, prepare a solution by diluting the RNase Stock Solution with cold ultrapure water to a final concentration of 0.20–0.30 Kunitz unit/mL.

    Technology detecting RNase activity

    A KAIST research team of Professor Hyun Gyu Park at Department of Chemical and Biomolecular Engineering developed a new technology to detect the activity of RNase H, a RNA degrading enzyme. The team used highly efficient signal amplification reaction termed catalytic hairpin assembly (CHA) to effectively analyze the RNase H activity. Considering that RNase H is required in the proliferation of retroviruses such as HIV, this research finding could contribute to AIDS treatments in the future, researchers say.

    This study led by Ph.D. candidates Chang Yeol Lee and Hyowon Jang was chosen as the cover for Nanoscale (Issue 42, 2017) published in 14 November.

    The existing techniques to detect RNase H require expensive fluorophore and quencher, and involve complex implementation. Further, there is no way to amplify the signal, leading to low detection efficiency overall. The team utilized CHA technology to overcome these limitations. CHA amplifies detection signal to allow more sensitive RNase H activity assay.

    The team designed the reaction system so that the product of CHA reaction has G-quadruplex structures, which is suitable to generate fluorescence. By using fluorescent molecules that bind to G-quadruplexes to generate strong fluorescence, the team could develop high performance RNase H detection method that overcomes the limitations of existing techniques. Further, this technology could screen inhibitors of RNase H activity.

    The team expects that the research finding could contribute to AIDS treatment. AIDS is disease caused by HIV, a retrovirus that utilizes reverse transcription, during which RNA is converted to DNA. RNase H is essential for reverse transcription in HIV, and thus inhibition of RNase H could in turn inhibit transcription of HIV DNA.

    Professor Park said, "This technology is applicable to detect various enzyme activities, as well as RNase H activity." He continued, "I hope this technology could be widely used in research on enzyme related diseases."


    Ethics declarations

    Competing interests

    The Regents of the University of California have patents issued and pending for CRISPR technologies on which H.S., B.F.C., G.J.K. and J.A.D. are inventors. J.A.D. is a cofounder of Caribou Biosciences, Editas Medicine, Scribe Therapeutics, Intellia Therapeutics and Mammoth Biosciences. J.A.D. is a scientific advisory board member of Caribou Biosciences, Intellia Therapeutics, eFFECTOR Therapeutics, Scribe Therapeutics, Mammoth Biosciences, Synthego, Algen Biotechnologies, Felix Biosciences and Inari. J.A.D. is a Director at Johnson & Johnson and has research projects sponsored by Biogen, Pfizer, AppleTree Partners and Roche.


    A Quadruplex-Based, Label-Free, and Real-Time Fluorescence Assay for RNase H Activity and Inhibition

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 (PR China), Fax: (+86) 0431-85262625

    Graduate School of the Chinese Academy of Sciences, Beijing, 100039 (PR China)

    Abstract

    We demonstrate a unique quadruplex-based fluorescence assay for sensitive, facile, real-time, and label-free detection of RNase H activity and inhibition by using a G-quadruplex formation strategy. In our approach, a RNA–DNA substrate was prepared, with the DNA strand designed as a quadruplex-forming oligomer. Upon cleavage of the RNA strand by RNase H, the released G-rich DNA strand folds into a quadruplex in the presence of monovalent ions and interacts with a specific G-quadruplex binder, N-methyl mesoporphyrin IX (NMM) this gives a dramatic increase in fluorescence and serves as a reporter of the reaction. This novel assay is simple in design, fast in operation, and is more convenient and promising than other methods. It takes less than 30 min to finish and the detection limit is much better or at least comparable to previous reports. No sophisticated experimental techniques or chemical modification for either RNA or DNA are required. The assay can be accomplished by using a common spectrophotometer and obviates possible interference with the kinetic behavior of the catalysts. Our approach offers an ideal system for high-throughput screening of enzyme inhibitors and demonstrates that the structure of the G-quadruplex can be used as a functional tool in specific fields in the future.

    Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors.

    Filename Description
    chem_200902166_sm_miscellaneous_information.pdf155 KB miscellaneous_information

    Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.


    Contents

    Bacterial RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein, called C5 protein. [4] [5] In vivo, both components are necessary for the ribozyme to function properly, but in vitro, the M1 RNA can act alone as a catalyst. [1] The primary role of the C5 protein is to enhance the substrate binding affinity and the catalytic rate of the M1 RNA enzyme probably by increasing the metal ion affinity in the active site. The crystal structure of a bacterial RNase P holoenzyme with tRNA has been recently resolved, showing how the large, coaxially stacked helical domains of the RNase P RNA engage in shape selective recognition of the pre-tRNA target. This crystal structure confirms earlier models of substrate recognition and catalysis, identifies the location of the active site, and shows how the protein component increases RNase P functionality. [6] [7]

    Bacterial RNase P class A and B Edit

    Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5'-ends of tRNAs by cleaving the 5'-leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins (RNP). RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the eubacterial ones, the RNA cores from all the three lineages are homologous—helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.

    In archaea, RNase P ribonucleoproteins consist of 4-5 protein subunits that are associated with RNA. As revealed by in vitro reconstitution experiments these protein subunits are individually dispensable for tRNA processing that is essentially mediated by the RNA component. [8] [9] [10] The structures of protein subunits of archaeal RNase P have been resolved by x-ray crystallography and NMR, thus revealing new protein domains and folding fundamental for function.

    Using comparative genomics and improved computational methods, a radically minimized form of the RNase P RNA, dubbed "Type T", has been found in all complete genomes in the crenarchaeal phylogenetic family Thermoproteaceae, including species in the genera Pyrobaculum, Caldivirga and Vulcanisaeta. [11] All retain a conventional catalytic domain, but lack a recognizable specificity domain. 5′ tRNA processing activity of the RNA alone was experimentally confirmed. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans-acting ribozymes. [11] Loss of the specificity domain in these RNAs suggests potential altered substrate specificity.

    It has recently been argued that the archaebacteriium Nanoarchaeum equitans does not possess RNase P. Computational and experimental studies failed to find evidence for its existence. In this organism the tRNA promoter is close to the tRNA gene and it is thought that transcription starts at the first base of the tRNA thus removing the requirement for RNase P. [12]

    In eukaryotes, such as humans and yeast, most RNase P consists of an RNA chain that is structurally similar to that found in bacteria [13] as well as nine to ten associated proteins (as opposed to the single bacterial RNase P protein, C5). [2] [14] Five of these protein subunits exhibit homology to archaeal counterparts. These protein subunits of RNase P are shared with RNase MRP, [14] [15] [16] a catalytic ribonucleoprotein involved in processing of ribosomal RNA in the nucleolus. [17] RNase P from eukaryotes was only recently demonstrated to be a ribozyme. [18] Accordingly, the numerous protein subunits of eucaryal RNase P have a minor contribution to tRNA processing per se, [19] while they seem to be essential for the function of RNase P and RNase MRP in other biological settings, such as gene transcription and the cell cycle. [3] [20] Despite the bacterial origins of mitochondria and chloroplasts, plastids from higher animals and plants do not appear to contain an RNA-based RNase P. It has been shown that human mitochondrial RNase P is a protein and does not contain RNA. [21] Spinach chloroplast RNase P has also been shown to function without an RNA subunit. [22]

    Subunits and functions of human RNase P [2]
    Subunit Function/interaction (in tRNA processing)
    RPP14 RNA binding
    RPP20 ATPase, helicase/Hsp27, SMN, Rpp25
    RPP21 RNA binding, activityg/Rpp29
    RPP25 RNA binding/Rpp20
    RPP29 tRNA binding, activity/Rpp21
    RPP30 RNA binding, activity/Pop5
    RPP38 RNA binding, activity
    RPP40
    hPop1
    hPop5 RNA binding, activity/Rpp30
    H1 RNA Activity/Rpp21, Rpp29, Rpp30, Rpp38

    RNase P is now being studied as a potential therapy for diseases such as herpes simplex virus, [23] cytomegalovirus, [23] [24] influenza and other respiratory infections, [25] HIV-1 [26] and cancer caused by fusion gene BCR-ABL. [23] [27] External guide sequences (EGSs) are formed with complementarity to viral or oncogenic mRNA and structures that mimic the T loop and acceptor stem of tRNA. [25] These structures allow RNase P to recognize the EGS and cleave the target mRNA. EGS therapies have shown to be effective in culture and in live mice. [28]


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