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The Genome Database for Rosaceae (GDR): year 10 update (2013)

Jung, S., Ficklin, S. P., Lee, T., Cheng, C.-H., Blenda, A., Zheng, P., Yu, J., Bombarely, A., Cho, I., Ru, S., Evans, K., Peace, C., Abbott, A. G., Mueller, L. A., Olmstead, M. A., Main, D.

Oxford University Press

In: Nucleic Acids Research

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Publikationsdatum: 2013-12-29

Beschreibung: The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org ), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse or download with a range of annotations, including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Genes and Genomes pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse. New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases. Synteny among the three sequenced genomes can be viewed using GBrowse_Syn. New markers, genetic maps and extensively curated qualitative/Mendelian and quantitative trait loci are available. Phenotype and genotype data from breeding projects and genetic diversity projects are also included. Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making.

Print ISSN: 0305-1048

Digitale ISSN: 1362-4962

Thema: Biologie

Publiziert von Oxford University Press

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Metal-induced DNA translocation leads to DNA polymerase conformational activation (2012)

Kirby, T. W., De; Rose, E. F., Cavanaugh, N. A., Beard, W. A., Shock, D. D., Mueller, G. A., Wilson, S. H., London, R. E.

Oxford University Press

In: Nucleic Acids Research

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Publikationsdatum: 2012-04-15

Beschreibung: Binding of the catalytic divalent ion to the ternary DNA polymerase β/gapped DNA/dNTP complex is thought to represent the final step in the assembly of the catalytic complex and is consequently a critical determinant of replicative fidelity. We have analyzed the effects of Mg 2+ and Zn 2+ on the conformational activation process based on NMR measurements of [methyl- 13 C]methionine DNA polymerase β. Unexpectedly, both divalent metals were able to produce a template base-dependent conformational activation of the polymerase/1-nt gapped DNA complex in the absence of a complementary incoming nucleotide, albeit with different temperature thresholds. This conformational activation is abolished by substituting Glu295 with lysine, thereby interrupting key hydrogen bonds necessary to stabilize the closed conformation. These and other results indicate that metal-binding can promote: translocation of the primer terminus base pair into the active site; expulsion of an unpaired pyrimidine, but not purine, base from the template-binding pocket; and motions of polymerase subdomains that close the active site. We also have performed pyrophosphorolysis studies that are consistent with predictions based on these results. These findings provide new insight into the relationships between conformational activation, enzyme activity and polymerase fidelity.

Print ISSN: 0305-1048

Digitale ISSN: 1362-4962

Thema: Biologie

Publiziert von Oxford University Press

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Nomenclature of steroidal sapogenins (1962)

Mueller, G. P. ; Pettit, G. R.

Springer

In: Experientia. 1962; 18(9): 404-405. Published 1962 Sep 01. doi: 10.1007/bf02151485.

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Publikationsdatum: 1962-09-01

Print ISSN: 0014-4754

Thema: Biologie , Medizin

Publiziert von Springer

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Genomic, RNAseq, and Molecular Modeling Evidence Suggests That the Major Allergen Domain in Insects Evolved from a Homodimeric Origin (2013)

Randall, T. A., Perera, L., London, R. E., Mueller, G. A.

Oxford University Press

In: Genome Biology and Evolution

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Publikationsdatum: 2013-12-12

Beschreibung: The major allergen domain (MA) is widely distributed in insects. The crystal structure of a single Bla g 1 MA revealed a novel protein fold in which the fundamental structure was a duplex of two subsequences (monomers), which had diverged over time. This suggested that the evolutionary origin of the MA structure may have been a homodimer of this smaller subsequence. Using publicly available genomic data, the distribution of the basic unit of this class of proteins was determined to better understand its evolutionary history. The duplication and divergence is examined at three distinct levels of resolution: 1) within the orders Diptera and Hymenoptera, 2) within one genus Drosophila , and 3) within one species Aedes aegypti . Within the family Culicidae, we have found two separate occurrences of monomers as independent genes. The organization of the gene family in A. aegypti shows a common evolutionary origin for its monomer and several closely related MAs. Molecular modeling of the A. aegypti monomer with the unique Bla g 1 fold confirms the distant evolutionary relationship and supports the feasibility of homodimer formation from a single monomer. RNAseq data for A. aegypti confirms that the monomer is expressed in the mosquito similar to other A. aegypti MAs after a blood meal. Together, these data support the contention that the detected monomer shares similar functional characteristics to related MAs in other insects. An extensive search for this domain outside of Insecta confirms that the MAs are restricted to insects.

Digitale ISSN: 1759-6653

Thema: Biologie

Publiziert von Oxford University Press

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Selective unfolding of one Ribonuclease H domain of HIV reverse transcriptase is linked to homodimer formation (2014)

Zheng, X., Pedersen, L. C., Gabel, S. A., Mueller, G. A., Cuneo, M. J., De; Rose, E. F., Krahn, J. M., London, R. E.

Oxford University Press

In: Nucleic Acids Research

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Publikationsdatum: 2014-05-01

Beschreibung: HIV-1 reverse transcriptase (RT), a critical enzyme of the HIV life cycle and an important drug target, undergoes complex and largely uncharacterized conformational rearrangements that underlie its asymmetric folding, dimerization and subunit-selective ribonuclease H domain (RH) proteolysis. In the present article we have used a combination of NMR spectroscopy, small angle X-ray scattering and X-ray crystallography to characterize the p51 and p66 monomers and the conformational maturation of the p66/p66' homodimer. The p66 monomer exists as a loosely structured molecule in which the fingers/palm/connection, thumb and RH substructures are connected by flexible (disordered) linking segments. The initially observed homodimer is asymmetric and includes two fully folded RH domains, while exhibiting other conformational features similar to that of the RT heterodimer. The RH' domain of the p66' subunit undergoes selective unfolding with time constant ~6.5 h, consistent with destabilization due to residue transfer to the polymerase' domain on the p66' subunit. A simultaneous increase in the intensity of resonances near the random coil positions is characterized by a similar time constant. Consistent with the residue transfer hypothesis, a construct of the isolated RH domain lacking the two N-terminal residues is shown to exhibit reduced stability. These results demonstrate that RH' unfolding is coupled to homodimer formation.

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Digitale ISSN: 1362-4962

Thema: Biologie

Publiziert von Oxford University Press

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Metal and ligand binding to the HIV-RNase H active site are remotely monitored by Ile556 (2012)

Zheng, X., Mueller, G. A., De; Rose, E. F., London, R. E.

Oxford University Press

In: Nucleic Acids Research

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Publikationsdatum: 2012-11-04

Beschreibung: HIV-1 reverse transcriptase (RT) contains a C-terminal ribonuclease H (RH) domain on its p66 subunit that can be expressed as a stable, although inactive protein. Recent studies of several RH enzymes demonstrate that substrate binding plays a major role in the creation of the active site. In the absence of substrate, the C-terminal helix E of the RT RNase H domain is dynamic, characterized by severe exchange broadening of its backbone amide resonances, so that the solution characterization of this region of the protein has been limited. Nuclear magnetic resonance studies of 13 C-labeled RH as a function of experimental conditions reveal that the 1 methyl resonance of Ile556, located in a short, random coil segment following helix E, experiences a large 13 C shift corresponding to a conformational change of Ile556 that results from packing of helix E against the central β-sheet. This shift provides a useful basis for monitoring the effects of various ligands on active site formation. Additionally, we report that the RNase H complexes formed with one or both divalent ions can be individually observed and characterized using diamagnetic Zn 2+ as a substitute for Mg 2+ . Ordering of helix E results specifically from the interaction with the lower affinity binding to the A divalent ion site.

Print ISSN: 0305-1048

Digitale ISSN: 1362-4962

Thema: Biologie

Publiziert von Oxford University Press

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