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Nakanishi K. When Argonaute takes out the ribonuclease sword. J Biol Chem 2024; 300:105499. [PMID: 38029964 PMCID: PMC10772731 DOI: 10.1016/j.jbc.2023.105499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
Argonaute (AGO) proteins in all three domains of life form ribonucleoprotein or deoxyribonucleoprotein complexes by loading a guide RNA or DNA, respectively. Since all AGOs retain a PIWI domain that takes an RNase H fold, the ancestor was likely an endoribonuclease (i.e., a slicer). In animals, most miRNA-mediated gene silencing occurs slicer independently. However, the slicer activity of AGO is indispensable in specific events, such as development and differentiation, which are critical for vertebrates and thus cannot be replaced by the slicer-independent regulation. This review highlights the distinctions in catalytic activation mechanisms among slicing-competent AGOs, shedding light on the roles of two metal ions in target recognition and cleavage. The precision of the target specificity by the RNA-induced silencing complexes is reevaluated and redefined. The possible coevolutionary relationship between slicer-independent gene regulation and AGO-binding protein, GW182, is also explored. These discussions reveal that numerous captivating questions remain unanswered regarding the timing and manner in which AGOs employ their slicing activity.
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Affiliation(s)
- Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
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2
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McQuarrie S, Athukoralage JS, McMahon SA, Graham S, Ackermann K, Bode BE, White MF, Gloster TM. Activation of Csm6 ribonuclease by cyclic nucleotide binding: in an emergency, twist to open. Nucleic Acids Res 2023; 51:10590-10605. [PMID: 37747760 DOI: 10.1093/nar/gkad739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023] Open
Abstract
Type III CRISPR systems synthesize cyclic oligoadenylate (cOA) second messengers as part of a multi-faceted immune response against invading mobile genetic elements (MGEs). cOA activates non-specific CRISPR ancillary defence nucleases to create a hostile environment for MGE replication. Csm6 ribonucleases bind cOA using a CARF (CRISPR-associated Rossmann Fold) domain, resulting in activation of a fused HEPN (Higher Eukaryotes and Prokaryotes Nucleotide binding) ribonuclease domain. Csm6 enzymes are widely used in a new generation of diagnostic assays for the detection of specific nucleic acid species. However, the activation mechanism is not fully understood. Here we characterised the cyclic hexa-adenylate (cA6) activated Csm6' ribonuclease from the industrially important bacterium Streptococcus thermophilus. Crystal structures of Csm6' in the inactive and cA6 bound active states illuminate the conformational changes which trigger mRNA destruction. Upon binding of cA6, there is a close to 60° rotation between the CARF and HEPN domains, which causes the 'jaws' of the HEPN domain to open and reposition active site residues. Key to this transition is the 6H domain, a right-handed solenoid domain connecting the CARF and HEPN domains, which transmits the conformational changes for activation.
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Affiliation(s)
- Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Januka S Athukoralage
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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3
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Noro I, Bettin I, Fasoli S, Smania M, Lunardi L, Giannini M, Andreoni L, Montioli R, Gotte G. Human RNase 1 can extensively oligomerize through 3D domain swapping thanks to the crucial contribution of its C-terminus. Int J Biol Macromol 2023; 249:126110. [PMID: 37536419 DOI: 10.1016/j.ijbiomac.2023.126110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Human ribonuclease (RNase) 1 and bovine RNase A are the proto-types of the secretory "pancreatic-type" (pt)-RNase super-family. RNase A can oligomerize through the 3D domain swapping (DS) mechanism upon acetic acid (HAc) lyophilisation, producing enzymatically active oligomeric conformers by swapping both N- and C-termini. Also some RNase 1 mutants were found to self-associate through 3D-DS, however forming only N-swapped dimers. Notably, enzymatically active dimers and larger oligomers of wt-RNase 1 were collected here, in higher amount than RNase A, from HAc lyophilisation. In particular, RNase 1 self-associates through the 3D-DS of its N-terminus and, at a higher extent, of the C-terminus. Since RNase 1 is four-residues longer than RNase A, we further analyzed its oligomerization tendency in a mutant lacking the last four residues. The C-terminus role has been investigated also in amphibian onconase (ONC®), a pt-RNase that can form only a N-swapped dimer, since its C-terminus, that is three-residues longer than RNase A, is locked by a disulfide bond. While ONC mutants designed to unlock or cut this constraint were almost unable to dimerize, the RNase 1 mutant self-associated at a higher extent than the wt, suggesting a specific role of the C-terminus in the oligomerization of different RNases. Overall, RNase 1 reaches here the highest ability, among pt-RNases, to extensively self-associate through 3D-DS, paving the way for new investigations on the structural and biological properties of its oligomers.
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Affiliation(s)
- Irene Noro
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Ilaria Bettin
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Sabrina Fasoli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Marcello Smania
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Luca Lunardi
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Michele Giannini
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Leonardo Andreoni
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Riccardo Montioli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
| | - Giovanni Gotte
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
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Ragucci S, Landi N, Citores L, Iglesias R, Russo R, Clemente A, Saviano M, Pedone PV, Chambery A, Ferreras JM, Di Maro A. The Biological Action and Structural Characterization of Eryngitin 3 and 4, Ribotoxin-like Proteins from Pleurotus eryngii Fruiting Bodies. Int J Mol Sci 2023; 24:14435. [PMID: 37833883 PMCID: PMC10572553 DOI: 10.3390/ijms241914435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Ribotoxin-like proteins (RL-Ps) are specific ribonucleases found in mushrooms that are able to cleave a single phosphodiester bond located in the sarcin-ricin loop (SRL) of the large rRNA. The cleaved SRL interacts differently with some ribosomal proteins (P-stalk). This action blocks protein synthesis because the damaged ribosomes are unable to interact with elongation factors. Here, the amino acid sequences of eryngitin 3 and 4, RL-Ps isolated from Pleurotus eryngii fruiting bodies, were determined to (i) obtain structural information on this specific ribonuclease family from edible mushrooms and (ii) explore the structural determinants which justify their different biological and antipathogenic activities. Indeed, eryngitin 3 exhibited higher toxicity with respect to eryngitin 4 against tumoral cell lines and model fungi. Structurally, eryngitin 3 and 4 consist of 132 amino acids, most of them identical and exhibiting a single free cysteinyl residue. The amino acidic differences between the two toxins are (i) an additional phenylalanyl residue at the N-terminus of eryngitin 3, not retrieved in eryngitin 4, and (ii) an additional arginyl residue at the C-terminus of eryngitin 4, not retrieved in eryngitin 3. The 3D models of eryngitins show slight differences at the N- and C-terminal regions. In particular, the positive electrostatic surface at the C-terminal of eryngitin 4 is due to the additional arginyl residue not retrieved in eryngitin 3. This additional positive charge could interfere with the binding to the SRL (substrate) or with some ribosomal proteins (P-stalk structure) during substrate recognition.
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Affiliation(s)
- Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (N.L.); (R.R.); (A.C.); (P.V.P.); (A.C.)
| | - Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (N.L.); (R.R.); (A.C.); (P.V.P.); (A.C.)
- Institute of Crystallography, National Research Council, Via Vivaldi 43, 81100 Caserta, Italy;
| | - Lucía Citores
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain; (L.C.); (R.I.); (J.M.F.)
| | - Rosario Iglesias
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain; (L.C.); (R.I.); (J.M.F.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (N.L.); (R.R.); (A.C.); (P.V.P.); (A.C.)
| | - Angela Clemente
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (N.L.); (R.R.); (A.C.); (P.V.P.); (A.C.)
| | - Michele Saviano
- Institute of Crystallography, National Research Council, Via Vivaldi 43, 81100 Caserta, Italy;
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (N.L.); (R.R.); (A.C.); (P.V.P.); (A.C.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (N.L.); (R.R.); (A.C.); (P.V.P.); (A.C.)
| | - José Miguel Ferreras
- Department of Biochemistry and Molecular Biology and Physiology, Faculty of Sciences, University of Valladolid, E-47011 Valladolid, Spain; (L.C.); (R.I.); (J.M.F.)
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, 81100 Caserta, Italy; (S.R.); (N.L.); (R.R.); (A.C.); (P.V.P.); (A.C.)
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5
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Wang F, Zhang C, Xu H, Zeng W, Ma L, Li Z. Structural Basis for the Ribonuclease Activity of a Thermostable CRISPR-Cas13a from Thermoclostridium caenicola. J Mol Biol 2023; 435:168197. [PMID: 37442412 DOI: 10.1016/j.jmb.2023.168197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/11/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
The RNA-targeting type VI CRISPR-Cas effector complexes are widely used in biotechnology applications such as gene knockdown, RNA editing, and molecular diagnostics. Compared with Cas13a from mesophilic organisms, a newly discovered Cas13a from thermophilic bacteria Thermoclostridium caenicola (TccCas13a) shows low sequence similarity, high thermostability, and lacks pre-crRNA processing activity. The thermostability of TccCas13a has been harnessed to make a sensitive and robust tool for nucleic acid detection. Here we present the structures of TccCas13a-crRNA binary complex at 2.8 Å, and TccCas13a at 3.5 Å. Although TccCas13a shares a similarly bilobed architecture with other mesophilic organism-derived Cas13a proteins, TccCas13a displayed distinct structure features. Specifically, it holds a long crRNA 5'-flank, forming extensive polar contacts with Helical-1 and HEPN2 domains. The detailed analysis of the interaction between crRNA 5'-flank and TccCas13a suggested lack of suitable nucleophile to attack the 2'-OH of crRNA 5'-flank may explain why TccCas13a fails to cleave pre-crRNA. The stem-loop segment of crRNA spacer toggles between double-stranded and single-stranded conformational states, suggesting a potential safeguard mechanism for target recognition. Superimposition of the structures of TccCas13a and TccCas13a-crRNA revealed several conformational changes required for crRNA loading, including dramatic movement of Helical-2 domain. Collectively, these structural insights expand our understanding into type VI CRISPR-Cas effectors, and would facilitate the development of TccCas13a-based applications.
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Affiliation(s)
- Feng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Haijiang Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanting Zeng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
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6
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Schroeder JW, Hurto RL, Randall JR, Wozniak KJ, Timko TA, Nye TM, Wang JD, Freddolino PL, Simmons LA. RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide. Sci Adv 2023; 9:eadi5945. [PMID: 37494439 PMCID: PMC10371020 DOI: 10.1126/sciadv.adi5945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
RNA:DNA hybrids compromise replication fork progression and genome integrity in all cells. The overall impacts of naturally occurring RNA:DNA hybrids on genome integrity, and the relative contributions of ribonucleases H to mitigating the negative effects of hybrids, remain unknown. Here, we investigate the contributions of RNases HII (RnhB) and HIII (RnhC) to hybrid removal, DNA replication, and mutagenesis genome wide. Deletion of either rnhB or rnhC triggers RNA:DNA hybrid accumulation but with distinct patterns of mutagenesis and hybrid accumulation. Across all cells, hybrids accumulate strongly in noncoding RNAs and 5'-UTRs of coding sequences. For ΔrnhB, hybrids accumulate preferentially in untranslated regions and early in coding sequences. We show that hybrid accumulation is particularly sensitive to gene expression in ΔrnhC cells. DNA replication in ΔrnhC cells is disrupted, leading to transversions and structural variation. Our results resolve the outstanding question of how hybrids in native genomic contexts cause mutagenesis and shape genome organization.
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Affiliation(s)
- Jeremy W. Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Rebecca L. Hurto
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Justin R. Randall
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Room 743E, Houston, TX 77030, USA
| | - Taylor A. Timko
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Taylor M. Nye
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jue D. Wang
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Levdansky Y, Raisch T, Deme JC, Pekovic F, Elmlund H, Lea SM, Valkov E. Structure and assembly of the NOT10:11 module of the CCR4-NOT complex. Commun Biol 2023; 6:739. [PMID: 37460791 PMCID: PMC10352241 DOI: 10.1038/s42003-023-05122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT remains poorly understood. Here, we present cryo-EM structures of human and chicken NOT1:NOT10:NOT11 ternary complexes to sub-3 Å resolution, revealing an evolutionarily conserved, flexible structure. Through biochemical dissection studies, which include the Drosophila orthologs, we show that the module assembly is hierarchical, with NOT11 binding to NOT10, which then organizes it for binding to NOT1. A short proline-rich motif in NOT11 stabilizes the entire module assembly.
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Affiliation(s)
- Yevgen Levdansky
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Filip Pekovic
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Hans Elmlund
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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8
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Ai Y, Li X, Wu X, Montalbán-López M, Zheng Z, Mu D. Secreting recombinant barnase by Lactococcus lactis and its application in reducing RNA from forages. Enzyme Microb Technol 2023; 164:110191. [PMID: 36608408 DOI: 10.1016/j.enzmictec.2022.110191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/18/2022] [Accepted: 12/29/2022] [Indexed: 01/02/2023]
Abstract
Barnase is a ribonuclease used for plasmid purification, targeted gene therapy and studies of protein interactions. To make the use of barnase easier, the barnase gene from Bacillus amyloliquefaciens BH072 was cloned into Lactococcus lactis under the control of the PP5 or PnisA promoters. Four recombinant expression vectors were constructed with one or two signal peptides to control the enzyme secretion. 310 mg/L barnase was obtained in the presence of its inhibitor barstar after 36 h induction. The properties of barnase were investigated, showing that the optimal reaction temperature and pH were 50 °C and 5.0, respectively, and the highest enzyme activity reached 16.5 kU/mL. Barnase stored at 40 °C for 72 h retained 90 % of its initial activity, and maintained more than 80 % of its initial activity after 72 h of storage at pH 5.0-9.0. Furthermore, the optimal conditions for enzymatic reduction of nucleic acids in single-cell proteins (SCP) forages was investigated. 1 % salt solution with an SCP-enzyme ratio of 1000:1, pH 5.0 and incubated at 50 °C for 1 h, allowed 82 % RNA content reduction. Finally, homology modeling of barnase demonstrates its three-dimensional structure, and substrate simulation docking predicts key active residues as well as bonding patterns.
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Affiliation(s)
- Yaqian Ai
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Xingjiang Li
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Xuefeng Wu
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Manuel Montalbán-López
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - Zhi Zheng
- Key Laboratory for Agricultural Products Processing of Anhui Province, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Dongdong Mu
- Anhui Fermented Food Engineering Research Center, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
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9
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Li H, Schneider T, Tan Y, Zhang D. Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases. Protein Sci 2023; 32:e4531. [PMID: 36477982 PMCID: PMC9793965 DOI: 10.1002/pro.4531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/07/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
Detection of homologous relationships among proteins and understanding their mechanisms of diversification are major topics in the fields of protein science, bioinformatics, and phylogenetics. Recent developments in sequence/profile-based and structural similarity-based methods have greatly facilitated the unification and classification of many protein families into superfamilies or folds, yet many proteins remain unclassified in current protein databases. As one of the three earliest identified RNases in biology, ribonuclease T2, also known as RNase I in Escherichia coli, RNase Rh in fungi, or S-RNase in plant, is thought to be an ancient RNase family due to its widespread distribution and distinct structure. In this study, we present evidence that RNase T2 represents a circularly permutated version of the BECR (Barnase-EndoU-Colicin E5/D-RelE) fold RNases. This subtle relationship cannot be detected by traditional methods such as sequence/profile-based comparisons, structure-similarity searches, and circular permutation detections. However, we were able to identify the structural similarity using rational reconstruction of a theoretical RNase T2 ancestor via a reverse circular permutation process, followed by structural modeling using AlphaFold2, and structural comparisons. This relationship is further supported by the fact that RNase T2 and other typical BECR RNases, namely Colicin D, RNase A, and BrnT, share similar catalytic site configurations, all involving an analogous set of conserved residues on the α0 helix and the β4 strand of the BECR fold. This study revealed a hidden root of RNase T2 in bacterial toxin systems and demonstrated that reconstruction and modeling of ancestral topology is an effective strategy to identify remote relationship between proteins.
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Affiliation(s)
- Huan Li
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
| | - Theresa Schneider
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
| | - Yongjun Tan
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
| | - Dapeng Zhang
- Department of BiologyCollege of Arts & Sciences, Saint Louis UniversitySaint LouisMissouriUSA
- Program of Bioinformatics and Computational BiologySchool of Science and Engineering, Saint Louis UniversitySaint LouisMissouriUSA
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Takebe K, Suzuki M, Sangawa T, Motoyoshi N, Itagaki T, Kashima K, Uzawa N, Kobayashi H. Identification of the Acidification Mechanism of the Optimal pH for RNase He1. Biol Pharm Bull 2023; 46:1778-1786. [PMID: 38044096 DOI: 10.1248/bpb.b23-00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Ribonuclease (RNase) He1 is a small ribonuclease belonging to the RNase T1 family. Most of the RNase T1 family members are active at neutral pH, except for RNase Ms, U2, and He1, which function at an acidic pH. We crystallized and analyzed the structure of RNase He1 and elucidated how the acidic amino residues of the α1β3- (He1:26-33) and β67-loops (He1:87-95) affect their optimal pH. In He1, Ms, and U2, the hydrogen bonding network formed by the acidic amino acids in the β67-loop suggested that the differences in the acidification mechanism of the optimum pH specified the function of these RNases. We found that the amino acid sequence of the β67-loop was not conserved and contributed to acidification of the optimum pH in different ways. Mutations in the acidic residues in He1 promoted anti-tumor growth activity, which clarified the role of these acidic amino residues in the binding pocket. These findings will enable the identification of additional targets for modifying pH-mediated enzymatic activities.
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Affiliation(s)
- Katsuki Takebe
- Oral & Maxillofacial Oncology and Surgery, Osaka University Graduate School of Dentistry
| | | | | | | | | | - Kana Kashima
- Oral & Maxillofacial Oncology and Surgery, Osaka University Graduate School of Dentistry
| | - Narikazu Uzawa
- Oral & Maxillofacial Oncology and Surgery, Osaka University Graduate School of Dentistry
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11
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Ulyanova V, Nadyrova A, Dudkina E, Kuznetsova A, Ahmetgalieva A, Faizullin D, Surchenko Y, Novopashina D, Zuev Y, Kuznetsov N, Ilinskaya O. Structural and Functional Differences between Homologous Bacterial Ribonucleases. Int J Mol Sci 2022; 23:ijms23031867. [PMID: 35163789 PMCID: PMC8837141 DOI: 10.3390/ijms23031867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 02/04/2023] Open
Abstract
Small cationic guanyl-preferring ribonucleases (RNases) produced by the Bacillus species share a similar protein tertiary structure with a high degree of amino acid sequence conservation. However, they form dimers that differ in conformation and stability. Here, we have addressed the issues (1) whether the homologous RNases also have distinctions in catalytic activity towards different RNA substrates and interactions with the inhibitor protein barstar, and (2) whether these differences correlate with structural features of the proteins. Circular dichroism and dynamic light scattering assays revealed distinctions in the structures of homologous RNases. The activity levels of the RNases towards natural RNA substrates, as measured spectrometrically by acid-soluble hydrolysis products, were similar and decreased in the row high-polymeric RNA >>> transport RNA > double-stranded RNA. However, stopped flow kinetic studies on model RNA substrates containing the guanosine residue in a hairpin stem or a loop showed that the cleavage rates of these enzymes were different. Moreover, homologous RNases were inhibited by the barstar with diverse efficiency. Therefore, minor changes in structure elements of homologous proteins have a potential to significantly effect molecule stability and functional activities, such as catalysis or ligand binding.
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Affiliation(s)
- Vera Ulyanova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
- Correspondence:
| | - Alsu Nadyrova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Elena Dudkina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Aleksandra Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Albina Ahmetgalieva
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Dzhigangir Faizullin
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (D.F.); (Y.Z.)
| | - Yulia Surchenko
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
| | - Darya Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (D.F.); (Y.Z.)
| | - Nikita Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.K.); (D.N.); (N.K.)
| | - Olga Ilinskaya
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia; (A.N.); (E.D.); (A.A.); (Y.S.); (O.I.)
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12
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Abstract
Many biomolecular condensates are thought to form via liquid-liquid phase separation (LLPS) of multivalent macromolecules. For those that form through this mechanism, our understanding has benefitted significantly from biochemical reconstitutions of key components and activities. Reconstitutions of RNA-based condensates to date have mostly been based on relatively simple collections of molecules. However, proteomics and sequencing data indicate that natural RNA-based condensates are enriched in hundreds to thousands of different components, and genetic data suggest multiple interactions can contribute to condensate formation to varying degrees. In this Perspective, we describe recent progress in understanding RNA-based condensates through different levels of biochemical reconstitutions as a means to bridge the gap between simple in vitro reconstitution and cellular analyses. Complex reconstitutions provide insight into the formation, regulation, and functions of multicomponent condensates. We focus on two RNA-protein condensate case studies: stress granules and RNA processing bodies (P bodies), and examine the evidence for cooperative interactions among multiple components promoting LLPS. An important concept emerging from these studies is that composition and stoichiometry regulate biochemical activities within condensates. Based on the lessons learned from stress granules and P bodies, we discuss forward-looking approaches to understand the thermodynamic relationships between condensate components, with the goal of developing predictive models of composition and material properties, and their effects on biochemical activities. We anticipate that quantitative reconstitutions will facilitate understanding of the complex thermodynamics and functions of diverse RNA-protein condensates.
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Affiliation(s)
- Simon L Currie
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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Koy C, Opuni KFM, Danquah BD, Neamtu A, Glocker MO. Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions. Int J Mol Sci 2021; 22:ijms221910183. [PMID: 34638522 PMCID: PMC8508491 DOI: 10.3390/ijms221910183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022] Open
Abstract
We investigated the influence of a solvent’s composition on the stability of desorbed and multiply charged RNAse S ions by analyzing the non-covalent complex’s gas-phase dissociation processes. RNAse S was dissolved in electrospray ionization-compatible buffers with either increasing organic co-solvent content or different pHs. The direct transition of all the ions and the evaporation of the solvent from all the in-solution components of RNAse S under the respective in-solution conditions by electrospray ionization was followed by a collision-induced dissociation of the surviving non-covalent RNAse S complex ions. Both types of changes of solvent conditions yielded in mass spectrometrically observable differences of the in-solution complexation equilibria. Through quantitative analysis of the dissociation products, i.e., from normalized ion abundances of RNAse S, S-protein, and S-peptide, the apparent kinetic and apparent thermodynamic gas-phase complex properties were deduced. From the experimental data, it is concluded that the stability of RNAse S in the gas phase is independent of its in-solution equilibrium but is sensitive to the complexes’ gas-phase charge states. Bio-computational in-silico studies showed that after desolvation and ionization by electrospray, the remaining binding forces kept the S-peptide and S-protein together in the gas phase predominantly by polar interactions, which indirectly stabilized the in-bulk solution predominating non-polar intermolecular interactions. As polar interactions are sensitive to in-solution protonation, bio-computational results provide an explanation of quantitative experimental data with single amino acid residue resolution.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
| | - Kwabena F. M. Opuni
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, P.O. Box LG43, Legon, Ghana
| | - Bright D. Danquah
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
| | - Andrei Neamtu
- Department of Physiology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Str. Universitatii nr. 16, 700051 Iasi, Romania;
| | - Michael O. Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
- Correspondence: ; Tel.: +49-381-494-4930; Fax: +49-381-494-4932
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14
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Pavlova AS, Yakovleva KI, Epanchitseva AV, Kupryushkin MS, Pyshnaya IA, Pyshnyi DV, Ryabchikova EI, Dovydenko IS. An Influence of Modification with Phosphoryl Guanidine Combined with a 2'-O-Methyl or 2'-Fluoro Group on the Small-Interfering-RNA Effect. Int J Mol Sci 2021; 22:ijms22189784. [PMID: 34575949 PMCID: PMC8467447 DOI: 10.3390/ijms22189784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Small interfering RNA (siRNA) is the most important tool for the manipulation of mRNA expression and needs protection from intracellular nucleases when delivered into the cell. In this work, we examined the effects of siRNA modification with the phosphoryl guanidine (PG) group, which, as shown earlier, makes oligodeoxynucleotides resistant to snake venom phosphodiesterase. We obtained a set of siRNAs containing combined modifications PG/2'-O-methyl (2'-OMe) or PG/2'-fluoro (2'-F); biophysical and biochemical properties were characterized for each duplex. We used the UV-melting approach to estimate the thermostability of the duplexes and RNAse A degradation assays to determine their stability. The ability to induce silencing was tested in cultured cells stably expressing green fluorescent protein. The introduction of the PG group as a rule decreased the thermodynamic stability of siRNA. At the same time, the siRNAs carrying PG groups showed increased resistance to RNase A. A gene silencing experiment indicated that the PG-modified siRNA retained its activity if the modifications were introduced into the passenger strand.
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Affiliation(s)
| | | | | | | | | | | | | | - Ilya S. Dovydenko
- Correspondence: (E.I.R.); (I.S.D.); Tel.: +7-383-363-5163 (E.I.R. & I.S.D.)
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15
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Hargett AA, Marcella AM, Yu H, Li C, Orwenyo J, Battistel MD, Wang LX, Freedberg DI. Glycosylation States on Intact Proteins Determined by NMR Spectroscopy. Molecules 2021; 26:molecules26144308. [PMID: 34299586 PMCID: PMC8303171 DOI: 10.3390/molecules26144308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022] Open
Abstract
Protein glycosylation is important in many organisms for proper protein folding, signaling, cell adhesion, protein-protein interactions, and immune responses. Thus, effectively determining the extent of glycosylation in glycoprotein therapeutics is crucial. Up to now, characterizing protein glycosylation has been carried out mostly by liquid chromatography mass spectrometry (LC-MS), which requires careful sample processing, e.g., glycan removal or protein digestion and glycopeptide enrichment. Herein, we introduce an NMR-based method to better characterize intact glycoproteins in natural abundance. This non-destructive method relies on exploiting differences in nuclear relaxation to suppress the NMR signals of the protein while maintaining glycan signals. Using RNase B Man5 and RNase B Man9, we establish reference spectra that can be used to determine the different glycoforms present in heterogeneously glycosylated commercial RNase B.
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Affiliation(s)
- Audra A. Hargett
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Aaron M. Marcella
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Huifeng Yu
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Jared Orwenyo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Marcos D. Battistel
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (C.L.); (J.O.); (L.-X.W.)
| | - Darón I. Freedberg
- Center for Biologics Evaluation and Review, Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (A.A.H.); (A.M.M.); (H.Y.); (M.D.B.)
- Correspondence:
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16
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Garcia-Rodriguez G, Charlier D, Wilmaerts D, Michiels J, Loris R. Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA. Nucleic Acids Res 2021; 49:7164-7178. [PMID: 34139012 PMCID: PMC8266594 DOI: 10.1093/nar/gkab513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/09/2021] [Accepted: 06/03/2021] [Indexed: 11/14/2022] Open
Abstract
The rnlAB toxin-antitoxin operon from Escherichia coli functions as an anti-phage defense system. RnlA was identified as a member of the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) superfamily of ribonucleases. The activity of the toxin RnlA requires tight regulation by the antitoxin RnlB, the mechanism of which remains unknown. Here we show that RnlA exists in an equilibrium between two different homodimer states: an inactive resting state and an active canonical HEPN dimer. Mutants interfering with the transition between states show that canonical HEPN dimerization via the highly conserved RX4-6H motif is required for activity. The antitoxin RnlB binds the canonical HEPN dimer conformation, inhibiting RnlA by blocking access to its active site. Single-alanine substitutions mutants of the highly conserved R255, E258, R318 and H323 show that these residues are involved in catalysis and substrate binding and locate the catalytic site near the dimer interface of the canonical HEPN dimer rather than in a groove located between the HEPN domain and the preceding TBP-like domain. Overall, these findings elucidate the structural basis of the activity and inhibition of RnlA and highlight the crucial role of conformational heterogeneity in protein function.
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Affiliation(s)
- Gabriela Garcia-Rodriguez
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium
- Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Dorien Wilmaerts
- Center of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001 Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Jan Michiels
- Center of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001 Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium
- Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium
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17
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Jankovic B, Ruf J, Zanobini C, Bozovic O, Buhrke D, Hamm P. Sequence of Events during Peptide Unbinding from RNase S: A Complete Experimental Description. J Phys Chem Lett 2021; 12:5201-5207. [PMID: 34038133 DOI: 10.1021/acs.jpclett.1c01155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The phototriggered unbinding of the intrinsically disordered S-peptide from the RNase S complex is studied with the help of transient IR spectroscopy, covering a wide range of time scales from 100 ps to 10 ms. To that end, an azobenzene moiety has been linked to the S-peptide in a way that its helicity is disrupted by light, thereby initiating its complete unbinding. The full sequence of events is observed, starting from unfolding of the helical structure of the S-peptide on a 20 ns time scale while still being in the binding pocket of the S-protein, S-peptide unbinding after 300 μs, and the structural response of the S-protein after 3 ms. With regard to the S-peptide dynamics, the binding mechanism can be classified as an induced fit, while the structural response of the S-protein is better described as conformational selection.
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Affiliation(s)
- Brankica Jankovic
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Claudio Zanobini
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - David Buhrke
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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18
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Siculella L, Giannotti L, Di Chiara Stanca B, Calcagnile M, Rochira A, Stanca E, Alifano P, Damiano F. Evidence for a Negative Correlation between Human Reactive Enamine-Imine Intermediate Deaminase A (RIDA) Activity and Cell Proliferation Rate: Role of Lysine Succinylation of RIDA. Int J Mol Sci 2021; 22:ijms22083804. [PMID: 33916919 PMCID: PMC8067581 DOI: 10.3390/ijms22083804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 01/17/2023] Open
Abstract
Reactive intermediate deaminase (Rid) proteins are enzymes conserved in all domains of life. UK114, a mammalian member of RidA subfamily, has been firstly identified as a component of liver perchloric acid-soluble proteins (L-PSP). Although still poorly defined, several functions have been attributed to the mammalian protein UK114/RIDA, including the reactive intermediate deamination activity. The expression of UK114/RIDA has been observed in some tumors, arousing interest in this protein as an evaluable tumor marker. However, other studies reported a negative correlation between UK114/RIDA expression, tumor differentiation degree and cell proliferation. This work addressed the question of UK114/RIDA expression in human non-tumor HEK293 cell lines and in some human tumor cell lines. Here we reported that human RIDA (hRIDA) was expressed in all the analyzed cell line and subjected to lysine (K-)succinylation. In HEK293, hRIDA K-succinylation was negatively correlated to the cell proliferation rate and was under the control of SIRT5. Moreover, K-succinylation clearly altered hRIDA quantification by immunoblotting, explaining, at least in part, some discrepancies about RIDA expression reported in previous studies. We found that hRIDA was able to deaminate reactive enamine-imine intermediates and that K-succinylation drastically reduced deaminase activity. As predicted by in silico analysis, the observed reduction of deaminase activity has been related to the drastic alterations of hRIDA structure inferred by K-succinylation. The role of hRIDA and the importance of its K-succinylation in cell metabolism, especially in cancer biology, have been discussed.
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Affiliation(s)
- Luisa Siculella
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
- Correspondence: (L.S.); (F.D.); Tel.: +39-0832-298-696 (L.S.); +39-0832-298-698 (F.D.)
| | - Laura Giannotti
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Benedetta Di Chiara Stanca
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Matteo Calcagnile
- Laboratory of Microbiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.C.); (P.A.)
| | - Alessio Rochira
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Eleonora Stanca
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
| | - Pietro Alifano
- Laboratory of Microbiology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (M.C.); (P.A.)
| | - Fabrizio Damiano
- Laboratory of Molecular Biology, Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (L.G.); (B.D.C.S.); (A.R.); (E.S.)
- Correspondence: (L.S.); (F.D.); Tel.: +39-0832-298-696 (L.S.); +39-0832-298-698 (F.D.)
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19
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Ye X, Axhemi A, Jankowsky E. Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces cerevisiae. RNA 2021; 27:465-476. [PMID: 33408095 PMCID: PMC7962489 DOI: 10.1261/rna.078006.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The 3' to 5' exonuclease Pop2p (Caf1p) is part of the CCR4-NOT deadenylation complex that removes poly(A) tails from mRNAs in cells. Pop2p is structurally conserved in eukaryotes, but Saccharomyces cerevisiae Pop2p harbors noncanonical amino acids in its catalytic center. The enzymatic properties of S. cerevisiae Pop2p are not well defined. Here we characterize the RNA exonuclease activity of recombinant S. cerevisiae Pop2p. We find that S. cerevisiae Pop2p degrades RNAs via two alternative reactions pathways, one generating nucleotides with 5'-phosphates and RNA intermediates with 3'-hydroxyls, and the other generating nucleotides with 3'-phosphates and RNA intermediates with 3'-phosphates. The enzyme is not able to initiate the reaction on RNAs with a 3'-phosphate, which leads to accumulation of RNAs with 3'-phosphates that can exceed 10 nt and are resistant to further degradation by S. cerevisiae Pop2p. We further demonstrate that S. cerevisiae Pop2p degrades RNAs in three reaction phases: an initial distributive phase, a second processive phase and a third phase during which processivity gradually declines. We also show that mutations of subsets of amino acids in the catalytic center, including those previously thought to inactivate the enzyme, moderately reduce, but not eliminate activity. Only mutation of all five amino acids in the catalytic center diminishes activity of Pop2p to background levels. Collectively, our results reveal robust exonuclease activity of S. cerevisiae Pop2p with unusual enzymatic properties, characterized by alternative degradation pathways, multiple reaction phases and functional redundancy of amino acids in the catalytic core.
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Affiliation(s)
- Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Armend Axhemi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Zhu W, McQuarrie S, Grüschow S, McMahon SA, Graham S, Gloster TM, White MF. The CRISPR ancillary effector Can2 is a dual-specificity nuclease potentiating type III CRISPR defence. Nucleic Acids Res 2021; 49:2777-2789. [PMID: 33590098 PMCID: PMC7969007 DOI: 10.1093/nar/gkab073] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
Cells and organisms have a wide range of mechanisms to defend against infection by viruses and other mobile genetic elements (MGE). Type III CRISPR systems detect foreign RNA and typically generate cyclic oligoadenylate (cOA) second messengers that bind to ancillary proteins with CARF (CRISPR associated Rossman fold) domains. This results in the activation of fused effector domains for antiviral defence. The best characterised CARF family effectors are the Csm6/Csx1 ribonucleases and DNA nickase Can1. Here we investigate a widely distributed CARF family effector with a nuclease domain, which we name Can2 (CRISPR ancillary nuclease 2). Can2 is activated by cyclic tetra-adenylate (cA4) and displays both DNase and RNase activity, providing effective immunity against plasmid transformation and bacteriophage infection in Escherichia coli. The structure of Can2 in complex with cA4 suggests a mechanism for the cA4-mediated activation of the enzyme, whereby an active site cleft is exposed on binding the activator. These findings extend our understanding of type III CRISPR cOA signalling and effector function.
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Affiliation(s)
- Wenlong Zhu
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
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21
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Bauer S, Yu D, Lawson AW, Saur IML, Frantzeskakis L, Kracher B, Logemann E, Chai J, Maekawa T, Schulze-Lefert P. The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold. PLoS Pathog 2021; 17:e1009223. [PMID: 33534797 PMCID: PMC7857584 DOI: 10.1371/journal.ppat.1009223] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVRA1, AVRA7, AVRA9, AVRA13, and allelic AVRA10/AVRA22, which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVRA6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVRA1, AVRA7, AVRA10/AVRA22, and AVRA13, suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVRA1 and AVRA6 as well as allelic AVRA10 and AVRA22 is largely determined by the receptors' C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVRA10 and five specific AVRA22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVRA effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.
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Affiliation(s)
- Saskia Bauer
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dongli Yu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne at Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Aaron W. Lawson
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Isabel M. L. Saur
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Elke Logemann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jijie Chai
- Institute of Biochemistry, University of Cologne at Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Takaki Maekawa
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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22
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Nowak I, Boratyn E, Student S, Bernhart SF, Fallmann J, Durbas M, Stadler PF, Rokita H. MCPIP1 ribonuclease can bind and cleave AURKA mRNA in MYCN-amplified neuroblastoma cells. RNA Biol 2021; 18:144-156. [PMID: 32757706 PMCID: PMC7834091 DOI: 10.1080/15476286.2020.1804698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/18/2020] [Accepted: 07/28/2020] [Indexed: 02/08/2023] Open
Abstract
The role of the inflammation-silencing ribonuclease, MCPIP1 (monocyte chemoattractant protein-induced protein 1), in neoplasia continuous to emerge. The ribonuclease can cleave not only inflammation-related transcripts but also some microRNAs (miRNAs) and viral RNAs. The suppressive effect of the protein has been hitherto suggested in breast cancer, clear cell renal cell carcinoma, osteosarcoma, and neuroblastoma. Our previous results have demonstrated a reduced levels of several oncogenes, as well as inhibited growth of neuroblastoma cells upon MCPIP1 overexpression. Here, we investigate the mechanisms underlying the suppression of MYCN proto-oncogene, bHLH transcription factor (MYCN)-amplified neuroblastoma cells overexpressing the MCPIP1 protein. We showed that the levels of several transcripts involved in cell cycle progression decreased in BE(2)-C and KELLY cells overexpressing MCPIP1 in a ribonucleolytic activity-dependent manner. However, RNA immunoprecipitation indicated that only AURKA mRNA (encoding for Aurora A kinase) interacts with the ribonuclease. Furthermore, the application of a luciferase assay suggested MCPIP1-dependent destabilization of the transcript. Further analyses demonstrated that the entire conserved region of AURKA seems to be indispensable for the interaction with the MCPIP1 protein. Additionally, we examined the effect of the ribonuclease overexpression on the miRNA expression profile in MYCN-amplified neuroblastoma cells. However, no significant alterations were observed. Our data indicate a key role of the binding and cleavage of the AURKA transcript in an MCPIP1-dependent suppressive effect on neuroblastoma cells.
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Affiliation(s)
- Iwona Nowak
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Elżbieta Boratyn
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sebastian Student
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Stephan F. Bernhart
- Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Małgorzata Durbas
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Hanna Rokita
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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23
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Ulyanova V, Dudkina E, Nadyrova A, Kalashnikov V, Surchenko Y, Ilinskaya O. The Cytotoxicity of RNase-Derived Peptides. Biomolecules 2020; 11:E16. [PMID: 33375305 PMCID: PMC7824363 DOI: 10.3390/biom11010016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial ribonuclease binase exhibits a cytotoxic effect on tumor cells possessing certain oncogenes. The aim of this study was to identify the structural parts of the binase molecule that exert cytotoxicity. Out of five designed peptides, the peptides representing the binase regions 21-50 and 74-94 have the highest cytotoxic potential toward human cervical HeLa and breast BT-20 and MCF-7 cancer cells. The peptides B21-50 and B74-94 were not able to enter human lung adenocarcinoma A549 cells, unlike BT-20 cells, explaining their failure to inhibit A549 cell proliferation. The peptide B74-94 shares similarities with epidermal growth factor (EGF), suggesting the peptide's specificity for EGF receptor overexpressed in BT-20 cells. Thus, the binase-derived peptides have the potential of being further developed as tumor-targeting peptides.
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Affiliation(s)
| | - Elena Dudkina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (V.U.); (A.N.); (V.K.); (Y.S.); (O.I.)
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24
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Baranzini N, Pulze L, Reguzzoni M, Roncoroni R, Orlandi VT, Tettamanti G, Acquati F, Grimaldi A. 3D Reconstruction of HvRNASET2 Molecule to Understand Its Antibacterial Role. Int J Mol Sci 2020; 21:E9722. [PMID: 33352806 PMCID: PMC7767213 DOI: 10.3390/ijms21249722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Recent studies performed on the invertebrate model Hirudo verbana (medicinal leech) suggest that the T2 ribonucleic enzyme HvRNASET2 modulates the leech's innate immune response, promoting microbial agglutination and supporting phagocytic cells recruitment in challenged tissues. Indeed, following injection of both lipoteichoic acid (LTA) and Staphylococcus aureus in the leech body wall, HvRNASET2 is expressed by leech type I granulocytes and induces bacterial aggregation to aid macrophage phagocytosis. Here, we investigate the HvRNASET2 antimicrobial role, in particular assessing the effects on the Gram-negative bacteria Escherichia coli. For this purpose, starting from the three-dimensional molecule reconstruction and in silico analyses, the antibacterial activity was evaluated both in vitro and in vivo. The changes induced in treated bacteria, such as agglutination and alteration in wall integrity, were observed by means of light, transmission and scanning electron microscopy. Moreover, immunogold, AMPs (antimicrobial peptides) and lipopolysaccharide (LPS) binding assays were carried out to evaluate HvRNASET2 interaction with the microbial envelopes and the ensuing ability to affect microbial viability. Finally, in vivo experiments confirmed that HvRNASET2 promotes a more rapid phagocytosis of bacterial aggregates by macrophages, representing a novel molecule for counteracting pathogen infections and developing alternative solutions to improve human health.
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Affiliation(s)
- Nicolò Baranzini
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Laura Pulze
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy;
| | - Rossella Roncoroni
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Viviana Teresa Orlandi
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Francesco Acquati
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Science, University of Insubria, 21100 Varese, Italy; (N.B.); (L.P.); (R.R.); (V.T.O.); (G.T.)
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25
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Freppel W, Merindol N, Rallu F, Bergevin M. Efficient SARS-CoV-2 detection in unextracted oro-nasopharyngeal specimens by rRT-PCR with the Seegene Allplex™ 2019-nCoV assay. Virol J 2020; 17:196. [PMID: 33339539 PMCID: PMC7746916 DOI: 10.1186/s12985-020-01468-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The fight against the COVID-19 pandemic has created an urgent need to rapidly detect infected people. The challenge for clinical laboratories has been finding a high throughput, cost-efficient, and accurate testing method in the context of extraction reagents shortage on a global scale. To answer this need, we studied SARS-CoV-2 detection in oro-nasopharyngeal (ONP) swabs stored in Universal Transport Media (UTM) or in RNase-free water by rRT-PCR with Seegene Allplex™ 2019-nCoV assay without RNA extraction. RESULTS Optimal results were obtained when swabs stored in UTM were diluted 1/5 and 1/2 in RNase-free water. Thermal lysis before rRT-PCR testing slightly improved detection rate. In addition, proteinase K (PK) treatment allowed for a significant reduction of invalid results and increased sensitivity for detection of low viral load specimens. In a panel of positive samples with all 3 viral genes amplified and N gene Cycle threshold values (Ct values) from 15 to 40, our detection rate was 98.9% with PK and 94.4% without. In a challenging panel of low positive samples with only the N gene being detectable at Ct values > 30, detection rate was increased from 53.3 to 76.7% with the addition of PK, and invalid rate fell off from 18.3 to 0%. Furthermore, we demonstrated that our method reliably detects specimens with Ct values up to 35, whereas false negative samples become frequent above this range. Finally, we show that swabs should be stored at - 70 °C rather than 4 °C when testing cannot be performed within 72 h of collection. CONCLUSION We successfully optimized the unextracted rRT-PCR process using the Seegene Allplex™ 2019-nCoV assay to detect SARS-CoV-2 RNAs in nasopharyngeal swabs. This improved method offers cost savings and turnaround time advantages compared to automated extraction, with high efficiency of detection that could play an important role in the surveillance of Covid-19.
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Affiliation(s)
- Wesley Freppel
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, QC, H7V 1B7, Canada
| | - Natacha Merindol
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
- Centre Intégré Universitaire de santé et services sociaux de la Mauricie et Centre du Québec, Trois-Rivières, QC, Canada
| | - Fabien Rallu
- Microbiology Department, Sainte-Justine Mother and Child University Hospital, Montréal, QC, Canada
| | - Marco Bergevin
- Département de biologie médicale Hôpital Cité-de-la-Santé, Laval, QC, H7M 3L9, Canada.
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26
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Raj R, Nadig S, Patel T, Gopal B. Structural and biochemical characteristics of two Staphylococcus epidermidis RNase J paralogs RNase J1 and RNase J2. J Biol Chem 2020; 295:16863-16876. [PMID: 32994223 PMCID: PMC7864078 DOI: 10.1074/jbc.ra120.014876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/21/2020] [Indexed: 11/06/2022] Open
Abstract
RNase J enzymes are metallohydrolases that are involved in RNA maturation and RNA recycling, govern gene expression in bacteria, and catalyze both exonuclease and endonuclease activity. The catalytic activity of RNase J is regulated by multiple mechanisms which include oligomerization, conformational changes to aid substrate recognition, and the metal cofactor at the active site. However, little is known of how RNase J paralogs differ in expression and activity. Here we describe structural and biochemical features of two Staphylococcus epidermidis RNase J paralogs, RNase J1 and RNase J2. RNase J1 is a homodimer with exonuclease activity aided by two metal cofactors at the active site. RNase J2, on the other hand, has endonuclease activity and one metal ion at the active site and is predominantly a monomer. We note that the expression levels of these enzymes vary across Staphylococcal strains. Together, these observations suggest that multiple interacting RNase J paralogs could provide a strategy for functional improvisation utilizing differences in intracellular concentration, quaternary structure, and distinct active site architecture despite overall structural similarity.
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Affiliation(s)
- Rishi Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Savitha Nadig
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Twinkal Patel
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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27
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Abstract
RNA offers nearly unlimited potential as a target for small molecule chemical probes and lead medicines. Many RNAs fold into structures that can be selectively targeted with small molecules. This Perspective discusses molecular recognition of RNA by small molecules and highlights key enabling technologies and properties of bioactive interactions. Sequence-based design of ligands targeting RNA has established rules for affecting RNA targets and provided a potentially general platform for the discovery of bioactive small molecules. The RNA targets that contain preferred small molecule binding sites can be identified from sequence, allowing identification of off-targets and prediction of bioactive interactions by nature of ligand recognition of functional sites. Small molecule targeted degradation of RNA targets (ribonuclease-targeted chimeras, RIBOTACs) and direct cleavage by small molecules have also been developed. These growing technologies suggest that the time is right to provide small molecule chemical probes to target functionally relevant RNAs throughout the human transcriptome.
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Affiliation(s)
- Matthew G Costales
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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28
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Shigemitsu H, Kubota R, Nakamura K, Matsuzaki T, Minami S, Aoyama T, Urayama K, Hamachi I. Protein-responsive protein release of supramolecular/polymer hydrogel composite integrating enzyme activation systems. Nat Commun 2020; 11:3859. [PMID: 32737298 PMCID: PMC7395795 DOI: 10.1038/s41467-020-17698-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/10/2020] [Indexed: 11/23/2022] Open
Abstract
Non-enzymatic proteins including antibodies function as biomarkers and are used as biopharmaceuticals in several diseases. Protein-responsive soft materials capable of the controlled release of drugs and proteins have potential for use in next-generation diagnosis and therapies. Here, we describe a supramolecular/agarose hydrogel composite that can release a protein in response to a non-enzymatic protein. A non-enzymatic protein-responsive system is developed by hybridization of an enzyme-sensitive supramolecular hydrogel with a protein-triggered enzyme activation set. In situ imaging shows that the supramolecular/agarose hydrogel composite consists of orthogonal domains of supramolecular fibers and agarose, which play distinct roles in protein entrapment and mechanical stiffness, respectively. Integrating the enzyme activation set with the composite allows for controlled release of the embedded RNase in response to an antibody. Such composite hydrogels would be promising as a matrix embedded in a body, which can autonomously release biopharmaceuticals by sensing biomarker proteins.
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Affiliation(s)
- Hajime Shigemitsu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Katsura, Kyoto, 615-8510, Japan
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Katsura, Kyoto, 615-8510, Japan
| | - Keisuke Nakamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Katsura, Kyoto, 615-8510, Japan
| | - Tomonobu Matsuzaki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Katsura, Kyoto, 615-8510, Japan
| | - Saori Minami
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan
| | - Takuma Aoyama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan
| | - Kenji Urayama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto, 606-8585, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Katsura, Kyoto, 615-8510, Japan.
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Nishikyo-ku, Kyoto, 615-8530, Japan.
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29
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Jolma A, Zhang J, Mondragón E, Morgunova E, Kivioja T, Laverty KU, Yin Y, Zhu F, Bourenkov G, Morris Q, Hughes TR, Maher LJ, Taipale J. Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences. Genome Res 2020; 30:962-973. [PMID: 32703884 PMCID: PMC7397871 DOI: 10.1101/gr.258848.119] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/23/2020] [Indexed: 01/09/2023]
Abstract
RNA-binding proteins (RBPs) regulate RNA metabolism at multiple levels by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation, and stability. Despite their central role in RNA function, the RNA-binding specificities of most RBPs remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and their RNA-binding domains (RBDs) and assessed their specificities using high-throughput RNA-SELEX (HTR-SELEX). Approximately 70% of RBPs for which we obtained a motif bound to short linear sequences, whereas ∼30% preferred structured motifs folding into stem-loops. We also found that many RBPs can bind to multiple distinctly different motifs. Analysis of the matches of the motifs in human genomic sequences suggested novel roles for many RBPs. We found that three cytoplasmic proteins-ZC3H12A, ZC3H12B, and ZC3H12C-bound to motifs resembling the splice donor sequence, suggesting that these proteins are involved in degradation of cytoplasmic viral and/or unspliced transcripts. Structural analysis revealed that the RNA motif was not bound by the conventional C3H1 RNA-binding domain of ZC3H12B. Instead, the RNA motif was bound by the ZC3H12B's PilT N terminus (PIN) RNase domain, revealing a potential mechanism by which unconventional RBDs containing active sites or molecule-binding pockets could interact with short, structured RNA molecules. Our collection containing 145 high-resolution binding specificity models for 86 RBPs is the largest systematic resource for the analysis of human RBPs and will greatly facilitate future analysis of the various biological roles of this important class of proteins.
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Affiliation(s)
- Arttu Jolma
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Solna, Sweden
| | - Jilin Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Solna, Sweden
| | - Estefania Mondragón
- Department of Biochemistry and Molecular Biology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, Minnesota 55905, USA
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Solna, Sweden
| | - Teemu Kivioja
- Genome-Scale Biology Program, University of Helsinki, FI-00014, Helsinki, Finland
| | - Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, M5S 1A8, Toronto, Canada
| | - Yimeng Yin
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Solna, Sweden
| | - Fangjie Zhu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Solna, Sweden
| | - Gleb Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, D-22603 Hamburg, Germany
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, M5S 1A8, Toronto, Canada
- Donnelly Centre, University of Toronto, M5S 3E1, Toronto, Canada
- Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, M5S 3G4, Toronto, Canada
- Department of Computer Science, University of Toronto, M5S 2E4, Toronto, Canada
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, M5S 1A8, Toronto, Canada
- Donnelly Centre, University of Toronto, M5S 3E1, Toronto, Canada
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, Minnesota 55905, USA
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Solna, Sweden
- Genome-Scale Biology Program, University of Helsinki, FI-00014, Helsinki, Finland
- Department of Biochemistry, University of Cambridge, CB2 1QW, Cambridge, United Kingdom
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30
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Abstract
Molecular recognition is a fundamental step in essentially any biological process. However, the kinetic processes during association and dissociation are difficult to be efficiently sampled by direct all-atom molecular dynamics simulations because of the large spatial and temporal scales. Here we propose an arbitrary resolution with two bead types (ART) coarse-grained (CG) strategy that is adept in molecular recognition. ART is a universal user-customized CG strategy that can generate a system-specific CG force field anytime and be applied to any system with an arbitrary CG resolution according to research requirements. ART CG simulations can be very efficiently performed with implicit solvation in prevalent simulation packages and provide interfaces for any enhanced sampling method. We used three applications, HLA-HIV epitope recognition, barnase-barstar association, and trimeric TRAF2 self-assembly, to validate the feasibility of the ART CG strategy, its advantages in protein recognition, and its high performance in simulations. Regular CG simulations can successfully achieve valid protein recognitions without any prior bound structure.
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Affiliation(s)
- Qinglu Zhong
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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31
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Guillen-Chable F, Rodríguez Corona U, Pereira-Santana A, Bayona A, Rodríguez-Zapata LC, Aquino C, Šebestová L, Vitale N, Hozak P, Castano E. Fibrillarin Ribonuclease Activity is Dependent on the GAR Domain and Modulated by Phospholipids. Cells 2020; 9:cells9051143. [PMID: 32384686 PMCID: PMC7290794 DOI: 10.3390/cells9051143] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
Fibrillarin is a highly conserved nucleolar methyltransferase responsible for ribosomal RNA methylation across evolution from Archaea to humans. It has been reported that fibrillarin is involved in the methylation of histone H2A in nucleoli and other processes, including viral progression, cellular stress, nuclear shape, and cell cycle progression. We show that fibrillarin has an additional activity as a ribonuclease. The activity is affected by phosphoinositides and phosphatidic acid and insensitive to ribonuclease inhibitors. Furthermore, the presence of phosphatidic acid releases the fibrillarin-U3 snoRNA complex. We show that the ribonuclease activity localizes to the GAR (glycine/arginine-rich) domain conserved in a small group of RNA interacting proteins. The introduction of the GAR domain occurred in evolution in the transition from archaea to eukaryotic cells. The interaction of this domain with phospholipids may allow a phase separation of this protein in nucleoli.
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Affiliation(s)
- Francisco Guillen-Chable
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Ulises Rodríguez Corona
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Alejandro Pereira-Santana
- Industrial Biotechnology Department, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Camino Arenero 1227, el Bajio, Zapopan C.P. 45019, Jalisco, Mexico;
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Alcaldia Benito Juarez C.P. 03940, Ciudad de Mexico, Mexico
| | - Andrea Bayona
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Luis Carlos Rodríguez-Zapata
- Biotechnology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatan, Mexico;
| | - Cecilia Aquino
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Lenka Šebestová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the CAS, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic; (L.Š.); (P.H.)
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Nicolas Vitale
- Institute of Celullar and Integrative Neuroscience (INCI), UPR-3212 The French National Centre for Scientific Research & University of Strasbourg, 67000 Strasbourg, France;
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the CAS, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic; (L.Š.); (P.H.)
| | - Enrique Castano
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
- Correspondence:
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32
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Buschauer R, Matsuo Y, Sugiyama T, Chen YH, Alhusaini N, Sweet T, Ikeuchi K, Cheng J, Matsuki Y, Nobuta R, Gilmozzi A, Berninghausen O, Tesina P, Becker T, Coller J, Inada T, Beckmann R. The Ccr4-Not complex monitors the translating ribosome for codon optimality. Science 2020; 368:eaay6912. [PMID: 32299921 PMCID: PMC8663607 DOI: 10.1126/science.aay6912] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/30/2020] [Accepted: 03/05/2020] [Indexed: 12/18/2022]
Abstract
Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.
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Affiliation(s)
- Robert Buschauer
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Yoshitaka Matsuo
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Takato Sugiyama
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ying-Hsin Chen
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Najwa Alhusaini
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Thomas Sweet
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ken Ikeuchi
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Jingdong Cheng
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Yasuko Matsuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Risa Nobuta
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Andrea Gilmozzi
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Petr Tesina
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Thomas Becker
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Jeff Coller
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany.
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33
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Abstract
Despite the recent advances in mass spectrometry (MS)-based methods for glycan structural analysis, characterization of glycomes remains a significant analytical challenge, in part due to the widespread presence of isomeric structures and the need to define the many structural variables for each glycan. Interpretation of the complex tandem mass spectra of glycans is often laborious and requires substantial expertise. Broad adoption of MS methods for glycomics, within and outside the glycoscience community, has been hindered by the shortage of bioinformatics tools for rapid and accurate glycan sequencing. Here, we developed an online porous graphitic carbon liquid chromatography (PGC-LC)-electronic excitation dissociation (EED) MS/MS method that takes advantage of the superior isomer resolving power of PGC and the structural details provided by EED MS/MS for characterization of glycan mixtures. We also made improvements to GlycoDeNovo, our de novo glycan sequencing algorithm, so that it can automatically and accurately identify glycan topologies from EED tandem mass spectra acquired online. The majority of linkages can also be determined de novo, although in some cases, biological insight may be needed to fully define the glycan structure. Application of this method to the analysis of N-glycans released from ribonuclease B not only revealed the presence of 18 high-mannose structures, including new isomers not previously reported, but also provided relative quantification for each isomeric structure. With fully automated data acquisition and topology analysis, the approach presented here holds great potential for automated and comprehensive glycan characterization.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
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34
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Gotte G, Menegazzi M. Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs. Front Immunol 2019; 10:2626. [PMID: 31849926 PMCID: PMC6901985 DOI: 10.3389/fimmu.2019.02626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marta Menegazzi
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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35
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Bocedi A, Cattani G, Gambardella G, Ticconi S, Cozzolino F, Di Fusco O, Pucci P, Ricci G. Ultra-Rapid Glutathionylation of Ribonuclease: Is this the Real Incipit of its Oxidative Folding? Int J Mol Sci 2019; 20:ijms20215440. [PMID: 31683668 PMCID: PMC6862303 DOI: 10.3390/ijms20215440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/16/2022] Open
Abstract
Many details of oxidative folding of proteins remain obscure, in particular, the role of oxidized glutathione (GSSG). This study reveals some unknown aspects. When a reduced ribonuclease A refolds in the presence of GSSG, most of its eight cysteines accomplish a very fast glutathionylation. In particular, one single cysteine, identified as Cys95 by mass spectrometry, displays 3600 times higher reactivity when compared with an unperturbed protein cysteine. Furthermore, the other five cysteines show 40-50 times higher reactivity toward GSSG. This phenomenon is partially due to a low pKa value of most of these cysteines (average pKa = 7.9), but the occurrence of a reversible GSSG-ribonuclease complex (KD = 0.12 mM) is reasonably responsible for the extraordinary hyper-reactivity of Cys95. Neither hyper-reactivity nor some protein-disulfide complexes have been found by reacting a reduced ribonuclease with other natural disulfides i.e., cystine, cystamine, and homocystine. Hyper-reactivity of all cysteines was observed toward 5,5'-dithiobis-(2-nitrobenzoic acid). Given that GSSG is present in high concentrations in the endoplasmic reticulum, this property may shed light on the early step of its oxidative folding. The ultra-rapid glutathionylation of cysteines, only devoted to form disulfides, is a novel property of the molten globule status of the ribonuclease.
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Affiliation(s)
- Alessio Bocedi
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", 00133 Rome, Italy.
| | - Giada Cattani
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", 00133 Rome, Italy.
| | - Giorgia Gambardella
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", 00133 Rome, Italy.
| | - Silvia Ticconi
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", 00133 Rome, Italy.
| | - Flora Cozzolino
- CEINGE Biotecnologie Avanzate and Department of Chemical Science, University of Naples "Federico II", 80126 Naples, Italy.
| | - Ornella Di Fusco
- CEINGE Biotecnologie Avanzate and Department of Chemical Science, University of Naples "Federico II", 80126 Naples, Italy.
| | - Piero Pucci
- CEINGE Biotecnologie Avanzate and Department of Chemical Science, University of Naples "Federico II", 80126 Naples, Italy.
| | - Giorgio Ricci
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", 00133 Rome, Italy.
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36
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Borchert AJ, Ernst DC, Downs DM. Reactive Enamines and Imines In Vivo: Lessons from the RidA Paradigm. Trends Biochem Sci 2019; 44:849-860. [PMID: 31103411 PMCID: PMC6760865 DOI: 10.1016/j.tibs.2019.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 01/19/2023]
Abstract
Metabolic networks are webs of integrated reactions organized to maximize growth and replication while minimizing the detrimental impact that reactive metabolites can have on fitness. Enamines and imines, such as 2-aminoacrylate (2AA), are reactive metabolites produced as short-lived intermediates in a number of enzymatic processes. Left unchecked, the inherent reactivity of enamines and imines may perturb the metabolic network. Genetic and biochemical studies have outlined a role for the broadly conserved reactive intermediate deaminase (Rid) (YjgF/YER057c/UK114) protein family, in particular RidA, in catalyzing the hydrolysis of enamines and imines to their ketone product. Herein, we discuss new findings regarding the biological significance of enamine and imine production and outline the importance of RidA in controlling the accumulation of reactive metabolites.
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Affiliation(s)
- Andrew J Borchert
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Dustin C Ernst
- Current address: Center for Circadian Biology, University of California, San Diego, San Diego, CA 92161, USA
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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37
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Santaus TM, Zhang F, Li S, Stine OC, Geddes CD. Effects of Lyse-It on endonuclease fragmentation, function and activity. PLoS One 2019; 14:e0223008. [PMID: 31568482 PMCID: PMC6768537 DOI: 10.1371/journal.pone.0223008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Nucleases are enzymes that can degrade genomic DNA and RNA that decrease the accuracy of quantitative measures of those nucleic acids. Here, we study conventional heating, standard microwave irradiation, and Lyse-It, a microwave-based lysing technology, for the potential to fragment and inactivate DNA and RNA endonucleases. Lyse-It employs the use of highly focused microwave irradiation to the sample ultimately fragmenting and inactivating RNase A, RNase B, and DNase I. Nuclease size and fragmentation were determined visually and quantitatively by SDS polyacrylamide gel electrophoresis and the mini-gel Agilent 2100 Bioanalyzer system, with a weighted size calculated to depict the wide range of nuclease fragmentation. Enzyme activity assays were conducted, and the rates were calculated to determine the effect of various lysing conditions on each of the nucleases. The results shown in this paper clearly demonstrate that Lyse-It is a rapid and highly efficient way to degrade and inactivate nucleases so that nucleic acids can be retained for down-stream detection.
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Affiliation(s)
- Tonya M. Santaus
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Fan Zhang
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Shan Li
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - O. Colin Stine
- Epidemiology and Public Health Department, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Chris D. Geddes
- Chemistry and Biochemistry Department, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
- Institute of Fluorescence, University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
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38
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Kim J, Mandal R, Hilty C. Observation of Fast Two-Dimensional NMR Spectra during Protein Folding Using Polarization Transfer from Hyperpolarized Water. J Phys Chem Lett 2019; 10:5463-5467. [PMID: 31442055 DOI: 10.1021/acs.jpclett.9b02197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nuclear spin hyperpolarized water is utilized to obtain protein spectra not only in the folded state but also during the refolding process. Polarization transfer to Ribonuclease Sa through proton exchange and the nuclear Overhauser effect (NOE) results in NMR signal enhancements of amide protons by up to 24-fold. These enhancements enable the measurement of fast two-dimensional NMR spectra on the same time scale as the folding. Resolved amide proton signals corresponding to the folded protein are observed both under folded and refolding conditions, whereby the refolding protein shows smaller transferred signals. Residue-specific evaluation of contributions to the polarization transfer indicates that signals attributed to a relayed intramolecular NOE are not observable in the refolding experiment. These differences are explained by the absence of long-range contacts and faster molecular motions in the unfolded protein. Applications of this method include accessing residue-specific information on structure and dynamics during multistate protein folding.
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Affiliation(s)
- Jihyun Kim
- Chemistry Department , Texas A&M University , 3255 TAMU, College Station , Texas 77843 , United States
| | - Ratnamala Mandal
- Chemistry Department , Texas A&M University , 3255 TAMU, College Station , Texas 77843 , United States
| | - Christian Hilty
- Chemistry Department , Texas A&M University , 3255 TAMU, College Station , Texas 77843 , United States
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Salazar VA, Arranz-Trullén J, Prats-Ejarque G, Torrent M, Andreu D, Pulido D, Boix E. Insight into the Antifungal Mechanism of Action of Human RNase N-terminus Derived Peptides. Int J Mol Sci 2019; 20:ijms20184558. [PMID: 31540052 PMCID: PMC6770517 DOI: 10.3390/ijms20184558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023] Open
Abstract
Candida albicans is a polymorphic fungus responsible for mucosal and skin infections. Candida cells establish themselves into biofilm communities resistant to most currently available antifungal agents. An increase of severe infections ensuing in fungal septic shock in elderly or immunosuppressed patients, along with the emergence of drug-resistant strains, urge the need for the development of alternative antifungal agents. In the search for novel antifungal drugs our laboratory demonstrated that two human ribonucleases from the vertebrate-specific RNaseA superfamily, hRNase3 and hRNase7, display a high anticandidal activity. In a previous work, we proved that the N-terminal region of the RNases was sufficient to reproduce most of the parental protein bactericidal activity. Next, we explored their potency against a fungal pathogen. Here, we have tested the N-terminal derived peptides that correspond to the eight human canonical RNases (RN1-8) against planktonic cells and biofilms of C. albicans. RN3 and RN7 peptides displayed the most potent inhibitory effect with a mechanism of action characterized by cell-wall binding, membrane permeabilization and biofilm eradication activities. Both peptides are able to eradicate planktonic and sessile cells, and to alter their gene expression, reinforcing its role as a lead candidate to develop novel antifungal and antibiofilm therapies.
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Affiliation(s)
- Vivian A Salazar
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Javier Arranz-Trullén
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - David Pulido
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
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40
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Walker DI, Cross LJ, Stapleton TA, Jenkins CL, Lees DN, Lowther JA. Assessment of the Applicability of Capsid-Integrity Assays for Detecting Infectious Norovirus Inactivated by Heat or UV Irradiation. Food Environ Virol 2019; 11:229-237. [PMID: 31165999 DOI: 10.1007/s12560-019-09390-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 05/25/2019] [Indexed: 05/27/2023]
Abstract
Human noroviruses are the leading cause of viral gastroenteritis. In the absence of a practical culture technique for routine analysis of infectious noroviruses, several methods have been developed to discriminate between infectious and non-infectious viruses by removing non-viable viruses prior to analysis by RT-qPCR. In this study, two such methods (RNase and porcine gastric mucin) which were designed to remove viruses with compromised capsids (and therefore assumed to be non-viable), were assessed for their ability to quantify viable F-specific RNA bacteriophage (FRNAP) and human norovirus following inactivation by UV-C or heat. It was found that while both methods could remove a proportion of non-viable viruses, a large proportion of non-viable virus remained to be detected by RT-qPCR, leading to overestimations of the viable population. A model was then developed to determine the proportion of RT-qPCR detectable RNA from non-viable viruses that must be removed by such methods to reduce overestimation to acceptable levels. In most cases, nearly all non-viable virus must be removed to reduce the log overestimation of viability to within levels that might be considered acceptable (e.g. below 0.5 log10). This model could be applied when developing alternative pre-treatment methods to determine how well they should perform to be comparable to established infectivity assays.
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Affiliation(s)
- David I Walker
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK.
| | - Lisa J Cross
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Tina A Stapleton
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Connaire L Jenkins
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - David N Lees
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - James A Lowther
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
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Matsumoto D, Tao R. Recognition of S-RNases by an S locus F-box like protein and an S haplotype-specific F-box like protein in the Prunus-specific self-incompatibility system. Plant Mol Biol 2019; 100:367-378. [PMID: 30937702 DOI: 10.1007/s11103-019-00860-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
S-RNase was demonstrated to be predominantly recognized by an S locus F-box-like protein and an S haplotype-specific F-box-like protein in compatible pollen tubes of sweet cherry. Self-incompatibility (SI) is a reproductive barrier that rejects self-pollen and inhibits self-fertilization to promote outcrossing. In Solanaceae and Rosaceae, S-RNase-based gametophytic SI (GSI) comprises S-RNase and F-box protein(s) as the pistil and pollen S determinants, respectively. Compatible pollen tubes are assumed to detoxify the internalized cytotoxic S-RNases to maintain growth. S-RNase detoxification is conducted by the Skp1-cullin1-F-box protein complex (SCF) formed by pollen S determinants, S locus F-box proteins (SLFs), in Solanaceae. In Prunus, the general inhibitor (GI), but not pollen S determinant S haplotype-specific F-box protein (SFB), is hypothesized to detoxify S-RNases. Recently, SLF-like proteins 1-3 (SLFL1-3) were suggested as GI candidates, although it is still possible that other proteins function predominantly in GI. To identify the other GI candidates, we isolated four other pollen-expressed SLFL and SFB-like (SFBL) proteins PavSLFL6, PavSLFL7A, PavSFBL1, and PavSFBL2 in sweet cherry. Binding assays with four PavS-RNases indicated that PavSFBL2 bound to PavS1, 6-RNase while the others bound to nothing. PavSFBL2 was confirmed to form an SCF complex in vitro. A co-immunoprecipitation assay using the recombinant PavS6-RNase as bait against pollen extracts and a mass spectrometry analysis identified the SCF complex components of PavSLFLs and PavSFBL2, M-locus-encoded glutathione S-transferase (MGST), DnaJ-like protein, and other minor proteins. These results suggest that SLFLs and SFBLs could act as predominant GIs in Prunus-specific S-RNase-based GSI.
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Affiliation(s)
- Daiki Matsumoto
- Laboratory of Pomology, Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan.
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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Harp JM, Guenther DC, Bisbe A, Perkins L, Matsuda S, Bommineni GR, Zlatev I, Foster DJ, Taneja N, Charisse K, Maier MA, Rajeev KG, Manoharan M, Egli M. Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity. Nucleic Acids Res 2019; 46:8090-8104. [PMID: 30107495 PMCID: PMC6144868 DOI: 10.1093/nar/gky703] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
Chemical modification is a prerequisite of oligonucleotide therapeutics for improved metabolic stability, uptake and activity, irrespective of their mode of action, i.e. antisense, RNAi or aptamer. Phosphate moiety and ribose C2′/O2′ atoms are the most common sites for modification. Compared to 2′-O-substituents, ribose 4′-C-substituents lie in proximity of both the 3′- and 5′-adjacent phosphates. To investigate potentially beneficial effects on nuclease resistance we combined 2′-F and 2′-OMe with 4′-Cα- and 4′-Cβ-OMe, and 2′-F with 4′-Cα-methyl modification. The α- and β-epimers of 4′-C-OMe-uridine and the α-epimer of 4′-C-Me-uridine monomers were synthesized and incorporated into siRNAs. The 4′α-epimers affect thermal stability only minimally and show increased nuclease stability irrespective of the 2′-substituent (H, F, OMe). The 4′β-epimers are strongly destabilizing, but afford complete resistance against an exonuclease with the phosphate or phosphorothioate backbones. Crystal structures of RNA octamers containing 2′-F,4′-Cα-OMe-U, 2′-F,4′-Cβ-OMe-U, 2′-OMe,4′-Cα-OMe-U, 2′-OMe,4′-Cβ-OMe-U or 2′-F,4′-Cα-Me-U help rationalize these observations and point to steric and electrostatic origins of the unprecedented nuclease resistance seen with the chain-inverted 4′β-U epimer. We used structural models of human Argonaute 2 in complex with guide siRNA featuring 2′-F,4′-Cα-OMe-U or 2′-F,4′-Cβ-OMe-U at various sites in the seed region to interpret in vitro activities of siRNAs with the corresponding 2′-/4′-C-modifications.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Dale C Guenther
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Lydia Perkins
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Donald J Foster
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Nate Taneja
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Martin A Maier
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
- To whom correspondence should be addressed. Tel: +1 615 343 8070; Fax: +1 615 343 0704; . Correspondence may also be addressed to Muthiah Manoharan. Tel: +1 617 551 8319; Fax: +1 617 551 8101;
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
- To whom correspondence should be addressed. Tel: +1 615 343 8070; Fax: +1 615 343 0704; . Correspondence may also be addressed to Muthiah Manoharan. Tel: +1 617 551 8319; Fax: +1 617 551 8101;
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Abstract
The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.
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Affiliation(s)
- Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland.
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, Geneva, Switzerland
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Zhang B, Ye Y, Ye W, Perčulija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S. Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Nat Commun 2019; 10:2544. [PMID: 31186424 PMCID: PMC6559982 DOI: 10.1038/s41467-019-10507-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/16/2019] [Indexed: 12/18/2022] Open
Abstract
Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.
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Affiliation(s)
- Bo Zhang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China
| | - Yangmiao Ye
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Weiwei Ye
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Han Jiang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yiyang Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yu Li
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Jing Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Jinying Lin
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Siqi Wang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Qi Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., 10617, Taipei, Taiwan
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
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Song H, Fan Y, Zhang J, Cooper AM, Silver K, Li D, Li T, Ma E, Zhu KY, Zhang J. Contributions of dsRNases to differential RNAi efficiencies between the injection and oral delivery of dsRNA in Locusta migratoria. Pest Manag Sci 2019; 75:1707-1717. [PMID: 30525311 DOI: 10.1002/ps.5291] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND The efficiency of RNA interference (RNAi) varies considerably among different insect species, and there is growing evidence to suggest that degradation of double-stranded (dsRNA) prior to uptake is an important factor that limits the efficiency of RNAi in insects. In Locusta migratoria, RNAi is highly efficient when dsRNA is delivered by injection, but not by feeding. However, detailed mechanisms causing such differential RNAi efficiency are still elusive. RESULTS We identified and characterized the full-length complementary DNAs (cDNAs) of two new dsRNA nuclease (dsRNase) genes from L. migratoria, which were named LmdsRNase1 and LmdsRNase4. Transcript analyses revealed that LmdsRNase1 and LmdsRNase4 were highly expressed in hemolymph with relatively lower expression in other tested tissues. Our study using heterologously expressed LmdsRNase1 and LmdsRNase4 fusion proteins showed that LmdsRNase1 can degrade dsRNA rapidly at an optimal pH of 5, whereas LmdsRNase4 had no activity at any of the pH values examined. In comparing the substrate specificity of the four LmdsRNases, we found that only LmdsRNase1 and LmdsRNase2 digested dsRNA; however, our experiments suggested that the physiological pH of hemolymph (7.0) suppresses LmdsRNase1 activity permitting significant dsRNA stability in this tissue. Conversely, the physiological pH of midgut juice (6.8) is ideal for LmdsRNase2 activity, resulting in degradation of dsRNA in midgut. CONCLUSION The physiological pH of different insect tissues or compartments can significantly alter the stability of dsRNA by influencing LmdsRNase activity in L. migratoria. Thus, new strategies to overcome such obstacles are expected to help implement RNAi-based technologies for insect pest management. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Huifang Song
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
- College of Life Science, Shanxi University, Taiyuan, China
| | - Yunhe Fan
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
- College of Life Science, Shanxi University, Taiyuan, China
| | - Jianqin Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | | | - Kristopher Silver
- Department of Entomology, Kansas State University, Manhattan, KS, USA
| | - Daqi Li
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
- Institute of Plant Protection, Shanxi Academy of Agricultural Science, Taiyuan, China
| | - Tao Li
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
| | - Enbo Ma
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, KS, USA
| | - Jianzhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, China
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46
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Wu R, Zhu Z, Xu X, Yu C, Li B. An investigation of solid-state nanopores on label-free metal-ion signalling via the transition of RNA-cleavage DNAzyme and the hybridization chain reaction. Nanoscale 2019; 11:10339-10347. [PMID: 31107481 DOI: 10.1039/c9nr01666j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances have proven solid-state nanopores as a powerful analysis platform that enables label-free and separation-free single-molecule analysis. However, the relatively low resolution still limits its application because many chemicals or targets with small sizes could not be recognized in a label-free condition. In this paper, we provide a possible solution that uses solid-state nanopores for small species signaling via the transition of huge DNA assembly products. DNAzyme responding to metal ions and the hybridization chain reaction (HCR) generating nanopore-detectable dsDNA concatamers are used as the transition model set. By the two-step DNAzyme-HCR transition, Pb2+ that was too tiny to be sensed was successfully recognized by the nanopore. The whole process happened in a completely homogeneous solution without any chemical modification. During condition optimization, we also discussed one possible application challenge that may affect the HCR signal-background distinction. Solid-state nanopores provide a potential solution to this challenge due to its ability to profile product length or even 3D structure information.
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Affiliation(s)
- Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China.
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47
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Dai Y, Peralta AN, Wynn JE, Sherpa C, Li H, Verma A, Le Grice SFJ, Santos WL. Molecular recognition of a branched peptide with HIV-1 Rev Response Element (RRE) RNA. Bioorg Med Chem 2019; 27:1759-1765. [PMID: 30879859 PMCID: PMC6476629 DOI: 10.1016/j.bmc.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 01/27/2023]
Abstract
Interaction of HIV-1 rev response element (RRE) RNA with its cognate protein, Rev, is critical for HIV-1 replication. Understanding the mode of interaction between RRE RNA and ligands at the binding site can facilitate RNA molecular recognition as well as provide a strategy for developing anti-HIV therapeutics. Our approach utilizes branched peptides as a scaffold for multivalent binding to RRE IIB (high affinity rev binding site) with incorporation of unnatural amino acids to increase affinity via non-canonical interactions with the RNA. Previous high throughput screening of a 46,656-member library revealed several hits that bound RRE IIB RNA in the sub-micromolar range. In particular, the lead compound, 4B3, displayed a Kd value of 410 nM and demonstrated selectivity towards RRE. A ribonuclease protection assay revealed that 4B3 binds to the stem-loop structure of RRE IIB RNA, which was confirmed by SHAPE analysis with 234 nt long NL4-3 RRE RNA. Our studies further indicated interaction of 4B3 with both primary and secondary Rev binding sites.
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Affiliation(s)
- Yumin Dai
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Ashley N Peralta
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Hao Li
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Astha Verma
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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Potenski CJ, Epshtein A, Bianco C, Klein HL. Genome instability consequences of RNase H2 Aicardi-Goutières syndrome alleles. DNA Repair (Amst) 2019; 84:102614. [PMID: 30975634 DOI: 10.1016/j.dnarep.2019.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/07/2023]
Abstract
The RNase H2 complex is a conserved heterotrimeric enzyme that degrades RNA:DNA hybrids and promotes excision of rNMPs misincorporated during DNA replication. Failure to remove ribonucleotides from DNA leads to genomic instability in yeast and humans. The monogenic Aicardi-Goutières syndrome (AGS) results from mutation in one of several genes, among which are those encoding the RNase H2 subunits. The complete cellular and genomic consequences of RNASEH2 mutations and the precise connection to disease remain unclear. To learn more about the effect of RNASEH2 mutations on the cell, we used yeast as a model of AGS disease. We have generated yeast strains bearing AGS-associated mutations in RNASEH2 genes. There is a range of disease presentation in patients bearing these RNASEH2 variants. Here we report on in vivo phenotypes of genomic instability, including mutation and recombination rates, and synthetic gene interactions. These phenotypes provide insight into molecular consequences of RNASEH2 mutations, and lay the groundwork for further study of genomic instability as a contributing factor to AGS disease.
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Affiliation(s)
- Catherine J Potenski
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Anastasiya Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Christopher Bianco
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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49
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Luige O, Murtola M, Ghidini A, Strömberg R. Further Probing of Cu 2+-Dependent PNAzymes Acting as Artificial RNA Restriction Enzymes. Molecules 2019; 24:molecules24040672. [PMID: 30769777 PMCID: PMC6412939 DOI: 10.3390/molecules24040672] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 11/16/2022] Open
Abstract
Peptide nucleic acid (PNA)-neocuproine conjugates have been shown to efficiently catalyse the cleavage of RNA target sequences in the presence of Cu2+ ions in a site-specific manner. These artificial enzymes are designed to force the formation of a bulge in the RNA target, the sequence of which has been shown to be key to the catalytic activity. Here, we present a further investigation into the action of Cu2+-dependent PNAzymes with respect to the dependence on bulge composition in 3- and 4-nucleotide bulge systems. Cu2+-dependent PNAzymes were shown to have a clear preference for 4-nucleotide bulges, as the cleavage of 3-nucleotide bulge-forming RNA sequences was significantly slower, which is illustrated by a shift in the half-lives from approximately 30 min to 24 h. Nonetheless, the nucleotide preferences at different positions in the bulge displayed similar trends in both systems. Moreover, the cleavage site was probed by introducing critical chemical modifications to one of the cleavage site nucleotides of the fastest cleaved 4-nucleotide RNA bulge. Namely, the exclusion of the exocyclic amine of the central adenine and the replacement of the 2′-hydroxyl nucleophile with 2′-H or 2′-OMe substituents in the RNA severely diminished the rate of RNA cleavage by the Cu2+-dependent PNAzyme, giving insight into the mechanism of cleavage. Moreover, the shorter recognition arm of the RNA/PNAzyme complex was modified by extending the PNAzyme by two additional nucleobases. The new PNAzyme was able to efficiently promote the cleavage of RNA when fully hybridised to a longer RNA target and even outperform the previous fastest PNAzyme. The improvement was demonstrated in cleavage studies with stoichiometric amounts of either PNAzyme present, and the extended PNAzyme was also shown to give turnover with a 10-fold excess of the RNA target.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland.
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
- Institut für Pharmazeutische Wissenschaften (IPW), Eidgenössische Technische Hochschule Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
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50
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Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV, Cheng DR, Scott DA. Functionally diverse type V CRISPR-Cas systems. Science 2019; 363:88-91. [PMID: 30523077 DOI: 10.1126/science.aav7271] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2024]
Abstract
Type V CRISPR-Cas systems are distinguished by a single RNA-guided RuvC domain-containing effector, Cas12. Although effectors of subtypes V-A (Cas12a) and V-B (Cas12b) have been studied in detail, the distinct domain architectures and diverged RuvC sequences of uncharacterized Cas12 proteins suggest unexplored functional diversity. Here, we identify and characterize Cas12c, -g, -h, and -i. Cas12c, -h, and -i demonstrate RNA-guided double-stranded DNA (dsDNA) interference activity. Cas12i exhibits markedly different efficiencies of CRISPR RNA spacer complementary and noncomplementary strand cleavage resulting in predominant dsDNA nicking. Cas12g is an RNA-guided ribonuclease (RNase) with collateral RNase and single-strand DNase activities. Our study reveals the functional diversity emerging along different routes of type V CRISPR-Cas evolution and expands the CRISPR toolbox.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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