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  1. Article ; Online: Molecular basis of Gabija anti-phage supramolecular assemblies.

    Yang, Xiao-Yuan / Shen, Zhangfei / Xie, Jiale / Greenwald, Jacelyn / Marathe, Ila / Lin, Qingpeng / Xie, Wen Jun / Wysocki, Vicki H / Fu, Tian-Min

    Nature structural & molecular biology

    2024  

    Abstract: As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of ... ...

    Abstract As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of Bacillus cereus GajA and GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.
    Language English
    Publishing date 2024-04-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-024-01283-w
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  2. Article ; Online: PtuA and PtuB assemble into an inflammasome-like oligomer for anti-phage defense.

    Li, Yuanyuan / Shen, Zhangfei / Zhang, Mengyuan / Yang, Xiao-Yuan / Cleary, Sean P / Xie, Jiale / Marathe, Ila A / Kostelic, Marius / Greenwald, Jacelyn / Rish, Anthony D / Wysocki, Vicki H / Chen, Chong / Chen, Qiang / Fu, Tian-Min / Yu, Yamei

    Nature structural & molecular biology

    2024  Volume 31, Issue 3, Page(s) 413–423

    Abstract: Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show that PtuA and PtuB form a stable complex with a 6:2 ... ...

    Abstract Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show that PtuA and PtuB form a stable complex with a 6:2 stoichiometry. Cryo-electron microscopy structure of PtuAB reveals a distinctive horseshoe-like configuration. PtuA adopts a hexameric arrangement, organized as an asymmetric trimer of dimers, contrasting the ring-like structure by other ATPases. Notably, the three pairs of PtuA dimers assume distinct conformations and fulfill unique roles in recruiting PtuB. Our functional assays have further illuminated the importance of the oligomeric assembly of PtuAB in anti-phage defense. Moreover, we have uncovered that ATP molecules can directly bind to PtuA and inhibit the activities of PtuAB. Together, the assembly and function of the Septu system shed light on understanding other ATPase-containing systems in bacterial immunity.
    MeSH term(s) Inflammasomes ; Cryoelectron Microscopy ; Bacteriophages/metabolism ; Adenosine Triphosphatases/metabolism ; Escherichia coli/metabolism
    Chemical Substances Inflammasomes ; Adenosine Triphosphatases (EC 3.6.1.-)
    Language English
    Publishing date 2024-01-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-023-01172-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Duplex Stem Replacement with bPNA+ Triplex Hybrid Stems Enables Reporting on Tertiary Interactions of Internal RNA Domains

    Miao, Shiqin / Liang, Yufeng / Marathe, Ila / Mao, Jie / DeSantis, Chris / Bong, Dennis

    Journal of the American Chemical Society. 2019 May 16, v. 141, no. 23

    2019  

    Abstract: We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA ... ...

    Abstract We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA affinity and hybrid thermostability can be obtained with half the molecular footprint of previously reported bPNA. Lysine derivatives bearing two melamine bases (K2M) can be prepared on multigram scale by double reductive alkylation with melamine acetaldehyde, resulting in a tertiary amine side chain that affords both peptide solubility and selective base-triple formation with 4 T/U bases; the Fmoc-K2M derivative can be used directly in solid phase peptide synthesis, rendering bPNA+ conveniently accessible. A compact bPNA+binding site of two U6 domains can be genetically encoded to replace existing 6 bp stem elements at virtually any location within an RNA transcript. We thus replaced internal 6 bp RNA stems that supported loop regions with 6 base-triple hybrid stems using fluorophore-labeled bPNA+. As the loop regions engaged in RNA tertiary interactions, the labeled hybrid stems provided a fluorescent readout; bPNA+ enabled this readout without covalent chemical modification or introduction of new structural elements. This strategy was demonstrated to be effective for reporting on widely observed RNA tertiary interactions such as intermolecular RNA–RNA kissing loop dimerization, RNA–protein binding, and intramolecular RNA tetraloop–tetraloop receptor binding, illustrating the potential general utility of this method. The modest 6 bp stem binding footprint of bPNA+ makes the hybrid stem replacement method practical for noncovalent installation of synthetic probes of RNA interactions. We anticipate that bPNA+ structural probes will be useful for the study of tertiary interactions in long noncoding RNAs.
    Keywords DNA ; acetaldehyde ; alkylation ; binding properties ; dimerization ; fluorescence ; hybrids ; lysine ; melamine ; messenger RNA ; non-coding RNA ; peptides ; solubility ; stems ; thermal stability
    Language English
    Dates of publication 2019-0516
    Size p. 9365-9372.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.9b03435
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  4. Article ; Online: Protein cofactors and substrate influence Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P.

    Marathe, Ila A / Lai, Stella M / Zahurancik, Walter J / Poirier, Michael G / Wysocki, Vicki H / Gopalan, Venkat

    Nucleic acids research

    2021  Volume 49, Issue 16, Page(s) 9444–9458

    Abstract: The ribonucleoprotein (RNP) form of archaeal RNase P comprises one catalytic RNA and five protein cofactors. To catalyze Mg2+-dependent cleavage of the 5' leader from pre-tRNAs, the catalytic (C) and specificity (S) domains of the RNase P RNA (RPR) ... ...

    Abstract The ribonucleoprotein (RNP) form of archaeal RNase P comprises one catalytic RNA and five protein cofactors. To catalyze Mg2+-dependent cleavage of the 5' leader from pre-tRNAs, the catalytic (C) and specificity (S) domains of the RNase P RNA (RPR) cooperate to recognize different parts of the pre-tRNA. While ∼250-500 mM Mg2+ renders the archaeal RPR active without RNase P proteins (RPPs), addition of all RPPs lowers the Mg2+ requirement to ∼10-20 mM and improves the rate and fidelity of cleavage. To understand the Mg2+- and RPP-dependent structural changes that increase activity, we used pre-tRNA cleavage and ensemble FRET assays to characterize inter-domain interactions in Pyrococcus furiosus (Pfu) RPR, either alone or with RPPs ± pre-tRNA. Following splint ligation to doubly label the RPR (Cy3-RPRC domain and Cy5-RPRS domain), we used native mass spectrometry to verify the final product. We found that FRET correlates closely with activity, the Pfu RPR and RNase P holoenzyme (RPR + 5 RPPs) traverse different Mg2+-dependent paths to converge on similar functional states, and binding of the pre-tRNA by the holoenzyme influences Mg2+ cooperativity. Our findings highlight how Mg2+ and proteins in multi-subunit RNPs together favor RNA conformations in a dynamic ensemble for functional gains.
    MeSH term(s) Archaea/enzymology ; Magnesium/metabolism ; Nucleic Acid Conformation/drug effects ; Pyrococcus furiosus/enzymology ; Pyrococcus furiosus/genetics ; RNA Precursors/genetics ; RNA, Archaeal/genetics ; RNA, Archaeal/ultrastructure ; RNA, Catalytic ; Ribonuclease P/genetics ; Ribonuclease P/ultrastructure
    Chemical Substances RNA Precursors ; RNA, Archaeal ; RNA, Catalytic ; Ribonuclease P (EC 3.1.26.5) ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 2021-08-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab655
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  5. Article ; Online: Duplex Stem Replacement with bPNA+ Triplex Hybrid Stems Enables Reporting on Tertiary Interactions of Internal RNA Domains.

    Miao, Shiqin / Liang, Yufeng / Marathe, Ila / Mao, Jie / DeSantis, Chris / Bong, Dennis

    Journal of the American Chemical Society

    2019  Volume 141, Issue 23, Page(s) 9365–9372

    Abstract: We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA ... ...

    Abstract We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA affinity and hybrid thermostability can be obtained with half the molecular footprint of previously reported bPNA. Lysine derivatives bearing two melamine bases (K
    MeSH term(s) DNA/chemistry ; Nucleic Acid Conformation ; Peptide Nucleic Acids/chemical synthesis ; Peptide Nucleic Acids/chemistry ; Peptides ; Protein Binding ; Protein Conformation ; RNA/chemistry
    Chemical Substances Peptide Nucleic Acids ; Peptides ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2019-05-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.9b03435
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Synthesis of Monodisperse Chitosan Nanoparticles and in Situ Drug Loading Using Active Microreactor.

    Kamat, Vivek / Marathe, Ila / Ghormade, Vandana / Bodas, Dhananjay / Paknikar, Kishore

    ACS applied materials & interfaces

    2015  Volume 7, Issue 41, Page(s) 22839–22847

    Abstract: Chitosan nanoparticles are promising drug delivery vehicles. However, the conventional method of unregulated mixing during ionic gelation limits their application because of heterogeneity in size and physicochemical properties. Therefore, a detailed ... ...

    Abstract Chitosan nanoparticles are promising drug delivery vehicles. However, the conventional method of unregulated mixing during ionic gelation limits their application because of heterogeneity in size and physicochemical properties. Therefore, a detailed theoretical analysis of conventional and active microreactor models was simulated. This led to design and fabrication of a polydimethylsiloxane microreactor with magnetic micro needles for the synthesis of monodisperse chitosan nanoparticles. Chitosan nanoparticles synthesized conventionally, using 0.5 mg/mL chitosan, were 250 ± 27 nm with +29.8 ± 8 mV charge. Using similar parameters, the microreactor yielded small size particles (154 ± 20 nm) at optimized flow rate of 400 μL/min. Further optimization at 0.4 mg/mL chitosan concentration yielded particles (130 ± 9 nm) with higher charge (+39.8 ± 5 mV). The well-controlled microreactor-based mixing generated highly monodisperse particles with tunable properties including antifungal drug entrapment (80%), release rate, and effective activity (MIC, 1 μg/mL) against Candida.
    MeSH term(s) Amphotericin B/pharmacology ; Antifungal Agents/pharmacology ; Candida/drug effects ; Chitosan/chemistry ; Computer Simulation ; Drug Liberation ; Endocytosis ; Humans ; MCF-7 Cells ; Materials Testing ; Microbial Sensitivity Tests ; Nanoparticles/chemistry ; Nanoparticles/ultrastructure ; Nanotechnology/instrumentation ; Particle Size ; Spectroscopy, Fourier Transform Infrared
    Chemical Substances Antifungal Agents ; Amphotericin B (7XU7A7DROE) ; Chitosan (9012-76-4)
    Language English
    Publishing date 2015-10-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.5b05100
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Synthesis of Monodisperse Chitosan Nanoparticles and in Situ Drug Loading Using Active Microreactor

    Kamat, Vivek / Bodas Dhananjay / Ghormade Vandana / Marathe Ila / Paknikar Kishore

    ACS Applied Materials & Interfaces. 2015 Oct. 21, v. 7, no. 41

    2015  

    Abstract: Chitosan nanoparticles are promising drug delivery vehicles. However, the conventional method of unregulated mixing during ionic gelation limits their application because of heterogeneity in size and physicochemical properties. Therefore, a detailed ... ...

    Abstract Chitosan nanoparticles are promising drug delivery vehicles. However, the conventional method of unregulated mixing during ionic gelation limits their application because of heterogeneity in size and physicochemical properties. Therefore, a detailed theoretical analysis of conventional and active microreactor models was simulated. This led to design and fabrication of a polydimethylsiloxane microreactor with magnetic micro needles for the synthesis of monodisperse chitosan nanoparticles. Chitosan nanoparticles synthesized conventionally, using 0.5 mg/mL chitosan, were 250 ± 27 nm with +29.8 ± 8 mV charge. Using similar parameters, the microreactor yielded small size particles (154 ± 20 nm) at optimized flow rate of 400 μL/min. Further optimization at 0.4 mg/mL chitosan concentration yielded particles (130 ± 9 nm) with higher charge (+39.8 ± 5 mV). The well-controlled microreactor-based mixing generated highly monodisperse particles with tunable properties including antifungal drug entrapment (80%), release rate, and effective activity (MIC, 1 μg/mL) against Candida.
    Keywords antifungal agents ; Candida ; chitosan ; drugs ; gelation ; mixing ; models ; nanoparticles ; physicochemical properties ; polydimethylsiloxane
    Language English
    Dates of publication 2015-1021
    Size p. 22839-22847.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1944-8252
    DOI 10.1021%2Facsami.5b05100
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: A novel double kink-turn module in euryarchaeal RNase P RNAs.

    Lai, Lien B / Tanimoto, Akiko / Lai, Stella M / Chen, Wen-Yi / Marathe, Ila A / Westhof, Eric / Wysocki, Vicki H / Gopalan, Venkat

    Nucleic acids research

    2017  Volume 45, Issue 12, Page(s) 7432–7440

    Abstract: RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn ( ... ...

    Abstract RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns. Mutagenesis of each of the putative K-turns singly or in combination decreased the number of bound L7Ae copies, and either eliminated or changed the L7Ae footprint on the mutant RPRs. In addition, our results support an unprecedented 'double K-turn' module in type A and type M archaeal RPR variants.
    MeSH term(s) Archaeal Proteins/chemistry ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Base Sequence ; Gene Expression Regulation, Archaeal ; Hydroxyl Radical/chemistry ; Hydroxyl Radical/metabolism ; Isoenzymes/chemistry ; Isoenzymes/genetics ; Isoenzymes/metabolism ; Methanocaldococcus/enzymology ; Methanocaldococcus/genetics ; Methanococcus/enzymology ; Methanococcus/genetics ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Pyrococcus furiosus/enzymology ; Pyrococcus furiosus/genetics ; RNA Precursors ; RNA, Archaeal/chemistry ; RNA, Archaeal/genetics ; RNA, Archaeal/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribonuclease P/chemistry ; Ribonuclease P/genetics ; Ribonuclease P/metabolism
    Chemical Substances Archaeal Proteins ; Isoenzymes ; RNA Precursors ; RNA, Archaeal ; Hydroxyl Radical (3352-57-6) ; RNA, Transfer (9014-25-9) ; Ribonuclease P (EC 3.1.26.5)
    Language English
    Publishing date 2017-07-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx388
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