cyclic phosphate
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2022 ◽  
Vol 0 (0) ◽  
Author(s):  
V. Janett Olzog ◽  
Lena I. Freist ◽  
Robin Goldmann ◽  
Jörg Fallmann ◽  
Christina E. Weinberg

Abstract Self-cleaving ribozymes are catalytic RNAs and can be found in all domains of life. They catalyze a site-specific cleavage that results in a 5′ fragment with a 2′,3′ cyclic phosphate (2′,3′ cP) and a 3′ fragment with a 5′ hydroxyl (5′ OH) end. Recently, several strategies to enrich self-cleaving ribozymes by targeted biochemical methods have been introduced by us and others. Here, we develop an alternative strategy in which 5ʹ OH RNAs are specifically ligated by RtcB ligase, which first guanylates the 3′ phosphate of the adapter and then ligates it directly to RNAs with 5′ OH ends. Our results demonstrate that adapter ligation to highly structured ribozyme fragments is much more efficient using the thermostable RtcB ligase from Pyrococcus horikoshii than the broadly applied Escherichia coli enzyme. Moreover, we investigated DNA, RNA and modified RNA adapters for their suitability in RtcB ligation reactions. We used the optimized RtcB-mediated ligation to produce RNA-seq libraries and captured a spiked 3ʹ twister ribozyme fragment from E. coli total RNA. This RNA-seq-based method is applicable to detect ribozyme fragments as well as other cellular RNAs with 5ʹ OH termini from total RNA.


2021 ◽  
Vol 54 (17) ◽  
pp. 7955-7962
Author(s):  
Soumabrata Majumdar ◽  
Brahim Mezari ◽  
Huiyi Zhang ◽  
Jeroen van Aart ◽  
Rolf A. T. M. van Benthem ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Megumi Shigematsu ◽  
Takuya Kawamura ◽  
Keisuke Morichika ◽  
Natsuko Izumi ◽  
Takashi Kiuchi ◽  
...  

AbstractIn animal germlines, PIWI proteins and the associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons. Here we report the extensive sequence and quantitative correlations between 2′,3′-cyclic phosphate-containing RNAs (cP-RNAs), identified using cP-RNA-seq, and piRNAs in the Bombyx germ cell line and mouse testes. The cP-RNAs containing 5′-phosphate (P-cP-RNAs) identified by P-cP-RNA-seq harbor highly consistent 5′-end positions as the piRNAs and are loaded onto PIWI protein, suggesting their direct utilization as piRNA precursors. We identified Bombyx RNase Kappa (BmRNase κ) as a mitochondria-associated endoribonuclease which produces cP-RNAs during piRNA biogenesis. BmRNase κ-depletion elevated transposon levels and disrupted a piRNA-mediated sex determination in Bombyx embryos, indicating the crucial roles of BmRNase κ in piRNA biogenesis and embryonic development. Our results reveal a BmRNase κ-engaged piRNA biogenesis pathway, in which the generation of cP-RNAs promotes robust piRNA production.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Monica C. Pillon ◽  
Meredith N. Frazier ◽  
Lucas B. Dillard ◽  
Jason G. Williams ◽  
Seda Kocaman ◽  
...  

AbstractNsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states. The cryo-EM reconstructions, combined with biochemistry, mass spectrometry, and molecular dynamics, expose molecular details of how critical active site residues recognize uridine and facilitate catalysis of the phosphodiester bond. Mass spectrometry revealed the accumulation of cyclic phosphate cleavage products, while analysis of the apo and UTP-bound datasets revealed conformational dynamics not observed by crystal structures that are likely important to facilitate substrate recognition and regulate nuclease activity. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.


2020 ◽  
Vol MA2020-02 (4) ◽  
pp. 691-691
Author(s):  
Qifeng Zheng ◽  
Yuki Yamada ◽  
Rui Shang ◽  
Eiichi Nakumura ◽  
Atsuo Yamada

FEBS Letters ◽  
2020 ◽  
Author(s):  
Christian Berk ◽  
Yuluan Wang ◽  
Artur Laski ◽  
Stylianos Tsagkris ◽  
Jonathan Hall

2020 ◽  
Vol 48 (18) ◽  
pp. 10397-10412
Author(s):  
Stephanie Jung ◽  
Tina von Thülen ◽  
Ines Yang ◽  
Viktoria Laukemper ◽  
Benjamin Rupf ◽  
...  

Abstract The RNA helicase RIG-I plays a key role in sensing pathogen-derived RNA. Double-stranded RNA structures bearing 5′-tri- or diphosphates are commonly referred to as activating RIG-I ligands. However, endogenous RNA fragments generated during viral infection via RNase L also activate RIG-I. Of note, RNase-digested RNA fragments bear a 5′-hydroxyl group and a 2′,3′-cyclic phosphate. How endogenous RNA fragments activate RIG-I despite the lack of 5′-phosphorylation has not been elucidated. Here we describe an endogenous RIG-I ligand (eRL) that is derived from the internal transcribed spacer 2 region (ITS2) of the 45S ribosomal RNA after partial RNase A digestion in vitro, RNase A protein transfection or RNase L activation. The immunostimulatory property of the eRL is dependent on 2′,3′-cyclic phosphate and its sequence is characterized by a G-quadruplex containing sequence motif mediating guanosine-5′-triphosphate (GTP) binding. In summary, RNase generated self-RNA fragments with 2′,3′-cyclic phosphate function as nucleotide-5′-triphosphate binding aptamers activating RIG-I.


IUBMB Life ◽  
2020 ◽  
Vol 72 (11) ◽  
pp. 2282-2289
Author(s):  
Heinrich K. Wasner
Keyword(s):  

RNA Biology ◽  
2020 ◽  
Vol 17 (8) ◽  
pp. 1060-1069 ◽  
Author(s):  
Megumi Shigematsu ◽  
Yohei Kirino

2020 ◽  
Vol 295 (25) ◽  
pp. 8514-8523
Author(s):  
Yue Yin ◽  
David Frank ◽  
Weijie Zhou ◽  
Neena Kaur ◽  
Jarrod B. French ◽  
...  

The suppressor of T-cell receptor (TCR) signaling (Sts) proteins Sts-1 and Sts-2 suppress receptor-mediated signaling pathways in various immune cells, including the TCR pathway in T cells and the Dectin-1 signaling pathway in phagocytes. As multidomain enzymes, they contain an N-terminal ubiquitin-association domain, a central Src homology 3 domain, and a C-terminal histidine phosphatase domain. Recently, a 2-histidine (2H) phosphoesterase motif was identified within the N-terminal portion of Sts. The 2H phosphoesterase motif defines an evolutionarily ancient protein domain present in several enzymes that hydrolyze cyclic phosphate bonds on different substrates, including cyclic nucleotides. It is characterized by two invariant histidine residues that play a critical role in catalytic activity. Consistent with its assignment as a phosphoesterase, we demonstrate here that the Sts-1 2H phosphoesterase domain displays catalytic, saturable phosphodiesterase activity toward the dinucleotide 2′,3′-cyclic NADP. The enzyme exhibited a high degree of substrate specificity and selectively generated the 3′-nucleotide as the sole product. Sts-1 also had phosphodiesterase catalytic activity toward a 5-mer RNA oligonucleotide containing a 2′,3′-cyclic phosphate group at its 3′ terminus. To investigate the functional significance of Sts-1 2H phosphoesterase activity, we generated His-to-Ala variants and examined their ability to negatively regulate cellular signaling pathways. Substitution of either conserved histidine compromised the ability of Sts-1 to suppress signaling pathways downstream of both the TCR and the Dectin-1 receptor. Our results identify a heretofore unknown cellular enzyme activity associated with Sts-1 and indicate that this catalytic activity is linked to specific cell-signaling outcomes.


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