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Adenines

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Bern Kohler – One of the best experts on this subject based on the ideXlab platform.

Bas Van Steensel – One of the best experts on this subject based on the ideXlab platform.

Ken F. Jarrell – One of the best experts on this subject based on the ideXlab platform.

  • bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M. Khursigara, Ken F. Jarrell
    Abstract:

    In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three adenine deletion version in the spontaneous mutant.

  • bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M. Khursigara, Ken F. Jarrell
    Abstract:

    In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three adenine deletion version in the spontaneous mutant.

Juan Niclosgutierrez – One of the best experts on this subject based on the ideXlab platform.

  • unravelling the versatile metal binding modes of adenine looking at the molecular recognition patterns of deaza and aza Adenines in mixed ligand metal complexes
    Coordination Chemistry Reviews, 2013
    Co-Authors: Alicia Dominguezmartin, Maria Pilar Brandiblanco, Antonio Matillahernandez, Hanan El Bakkali, Valeria Marina Nurchi, Josefa Maria Gonzalezperez, Alfonso Castineiras, Juan Niclosgutierrez
    Abstract:

    Abstract To better understand the extreme versatility of adenine as a ligand, the metal binding patterns of some closely related N-ligands have been carefully analysed. All the selected ligands comply with the requirement of having at least one N-heterocyclic atom in each cycle of the purine skeleton. The N-ligands are: (a) deaza-Adenines [7-azaindole (H7azain), 4-azabenzimidazole (H4abim), 5-azabenzimidazole (H5abim), 7-deaza-adenine (H7deaA), purine (Hpur)] (b) adenine isomers [2-aminopurine (H2AP), 4-aminopyrazolo[3,4- d ]pyrimidine (H4app), 7-amino[1,2,4]triazolo[1,5- a ]pyrimidine (7atp)] and (c) aza-Adenines [2,6-diaminopurine (Hdap), 8-aza-adenine (H8aA)]. The different molecular recognition patterns are reviewed on the basis of the available structural information in the Cambridge Structural Database, version 5.33 (updated Nov. 2012). No restraints have been placed concerning the neutral or charged species of these N-ligands or the metal ions involved in the coordination. Attention is paid to the proton tautomerism and its metal binding patterns, highlighting many examples where the molecular recognition pattern is carried out by the cooperation of a metal N bond and an intra-molecular inter-ligand H-bonding interaction.

  • structural insights on the molecular recognition patterns between n 6 substituted Adenines and n aryl methyl iminodiacetate copper ii chelates
    Journal of Inorganic Biochemistry, 2013
    Co-Authors: Alicia Dominguezmartin, Antonio Matillahernandez, Alfonso Castineiras, Angel Garciaraso, Catalina Cabot, Duane Choquesillolazarte, Inmaculada Pereztoro, Juan Niclosgutierrez
    Abstract:

    Abstract For a better understanding of the metal binding pattern of N6-substituted Adenines, six novel ternary Cu(II) complexes have been structurally characterized by single crystal X-ray diffraction: [Cu(NBzIDA)(HCy5ade)(H2O)] · H2O (1), [Cu(NBzIDA)(HCy6ade)(H2O)] · H2O (2), [Cu(FurIDA)(HCy6ade)(H2O)] · H2O (3), [Cu(MEBIDA)(HBAP)(H2O)] · H2O (4), [Cu(FurIDA)(HBAP)]n (5) and {[Cu(NBzIDA)(HdimAP)] · H2O}n (6). In these compounds NBzIDA, FurIDA and MEBIDA are N-substituted iminodiacetates with a non-coordinating aryl-methyl pendant arm (benzyl in NBzIDA, p-tolyl in MEBIDA and furfuryl in FurIDA) whereas HBAP, HCy5ade, HCy6ade and HdimAP are N6-substituted adenine derivatives with a N-benzyl, N-cyclopentyl, N-cyclohexyl or two N-methyl groups, respectively. Regardless of the molecular (1–4) or polymeric (5–6) nature of the studied compounds, the Cu(II) centre exhibits a type 4 + 1 coordination where the tridentate IDA-like chelators adopt a mer-conformation. In 1–5 the N6-R-Adenines use their most stable tautomer H(N9)adenine-like, and molecular recognition consists of the cooperation of the Cu N3(purine) bond and the intra-molecular interligand N9 H · · · O(coordinated carboxy) interaction. In contrast, N6,N6-dimethyl-adenine shows the rare tautomer H(N3)dimAP in 6, so that the molecular recognition with the Cu(NBzIDA) chelate consist of the Cu N9 bond and the N3 H · · · O intra-molecular interligand interaction. Contrastingly to the cytokinin activity found in the free ligands HBAP (natural cytokinin), HCy5ade and HCy6ade, the corresponding Cu(II) ternary complexes did not show any activity.

Partho Ghosh – One of the best experts on this subject based on the ideXlab platform.

  • T. aquaticus DGR.
    , 2019
    Co-Authors: Sumit Handa, Kharissa L. Shaw, Partho Ghosh
    Abstract:

    The T. aquaticus prophage DGR contains a gene encoding a variable protein (taqvp). The 3’ end of taqvp contains the variable region (VR) and initiation-of-mutagenic homing (IMH) sequence. The DGR also contains an accessory variability determinant (avd) gene, followed by an invariant template region (TR), which differs from VR mainly at Adenines. A sequence similar but not identical to the VR IMH occurs at the 3’ end of the TR and is called IMH*. Following these elements is a gene encoding a reverse trantranscriptase (rt). TR is transcribed to produce TR-RNA, which is reverse transcribed to produce TR-cDNA, with adenine-specific mutagenesis of the sequence accompanying reverse transcription. Adenine-mutagenized TR-cDNA homes to and replaces VR to yield a variant TaqVP.

  • template assisted synthesis of adenine mutagenized cdna by a retroelement protein complex
    Nucleic Acids Research, 2018
    Co-Authors: Sumit Handa, Yong Jiang, Robert Foreman, Raymond F Schinazi, Jeff F Miller, Partho Ghosh
    Abstract:

    Author(s): Handa, Sumit; Jiang, Yong; Tao, Sijia; Foreman, Robert; Schinazi, Raymond; Miller, Jeff; Ghosh, Partho | Abstract: ABSTRACT Diversity-generating retroelements (DGRs) create unparalleled levels of protein sequence variation through mutagenic retrohoming. Sequence information is transferred from an invariant template region ( TR ), through an RNA intermediate, to a protein-coding variable region. Selective infidelity at Adenines during transfer is a hallmark of DGRs from disparate bacteria, archaea, and microbial viruses. We recapitulated selective infidelity in vitro for the prototypical Bordetella bacteriophage DGR. A complex of the DGR reverse trantranscriptase bRT and pentameric accessory variability determinant (Avd) protein along with DGR RNA were necessary and sufficient for synthesis of template-primed, covalently linked RNA-cDNA molecules, as observed in vivo . We identified RNAcDNA molecules to be branched and most plausibly linked through 2′-5′ phosphodiester bonds. Adeninemutagenesis was intrinsic to the bRT-Avd complex, which displayed unprecedented promiscuity while reverse transcribing Adenines of either DGR or non-DGR RNA templates. In contrast, bRT-Avd processivity was strictly dependent on the template, occurring only for the DGR RNA. This restriction was mainly due to a noncoding segment downstream of TR , which specifically bound Avd and created a privileged site for processive polymerization. Restriction to DGR RNA may protect the host genome from damage. These results define the early steps in a novel pathway for massive sequence diversification.

  • template assisted synthesis of adenine mutagenized cdna by a retroelement protein complex
    bioRxiv, 2018
    Co-Authors: Sumit Handa, Yong Jiang, Robert Foreman, Raymond F Schinazi, Jeff F Miller, Partho Ghosh
    Abstract:

    Diversity-generating retroelements (DGRs) create unparalleled levels of protein sequence variation through mutagenic retrohoming. Sequence information is transferred from an invariant template region (TR), through an RNA intermediate, to a protein-coding variable region. Selective infidelity at Adenines during transfer is a hallmark of DGRs from disparate bacteria, archaea, and microbial viruses. We recapitulated selective infidelity in vitro for the prototypical Bordetella bacteriophage DGR. A complex of the DGR reverse trantranscriptase bRT and pentameric accessory variability determinant (Avd) protein along with DGR RNA were necessary and sufficient for synthesis of template-primed, covalently linked RNA-cDNA molecules, as observed in vivo. We identified RNA-cDNA molecules to be branched and most plausibly linked through 29-59 phosphodiester bonds. Adeninemutagenesis was intrinsic to the bRT-Avd complex, which displayed unprecedented promiscuity while reverse transcribing Adenines of either DGR or non-DGR RNA templates. In contrast, bRT-Avd processivity was strictly dependent on the template, occurring only for the DGR RNA. This restriction was mainly due to a noncoding segment downstream of TR, which specifically bound Avd and created a privileged site for processive polymerization. Restriction to DGR RNA may protect the host genome from damage. These results define the early steps in a novel pathway for massive sequence diversification.