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  • 1
    Language: English
    In: The Journal of biological chemistry, 19 January 2018, Vol.293(3), pp.920-930
    Description: Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the and BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases.
    Keywords: Anbu ; Bph ; Hslv ; Proteasome ; Protein Crystallization ; Protein Degradation ; Protein Evolution ; Protein Structure ; Small-Angle X-Ray Scattering (Saxs) ; Proteasome Endopeptidase Complex -- Chemistry
    E-ISSN: 1083-351X
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  • 2
    Language: English
    In: Structure, 01 August 2017, Vol.25(8), pp.1303-1309.e3
    Description: African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved. Hipp et al. have determined the structure of African cassava mosaic virus at 4.2 Å and described the intra- and inter-capsomer contacts that help to partly explain the unusual twin particle structure. The authors have found a new pocket for possible DNA binding.
    Keywords: Geminivirus ; Virus Particles ; Electron Cryomicroscopy ; Modeling ; Acmv ; Image Processing ; Structure ; Biology
    ISSN: 0969-2126
    E-ISSN: 1878-4186
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  • 3
    Language: English
    In: Virology, November 2016, Vol.498, pp.136-148
    Description: Plant infecting geminiviruses encode a small (A)C4 protein within the open reading frame of the replication-initiator protein. In African cassava mosaic virus, two in-frame start codons may be used for the translation of a longer and a shorter AC4 variant. Both were fused to green fluorescent protein or glutathione-S-transferase genes and expressed in fission yeast. The longer variant accumulated in discrete spots in the cytoplasm, whereas the shorter variant localized to the plasma membrane. A similar expression pattern was found in plants. A myristoylation motif may promote a targeting of the shorter variant to the plasma membrane. Mass spectrometry analysis of the yeast-expressed shorter variant detected the corresponding myristoylation. The biological relevance of the second start codon was confirmed using mutated infectious clones. Whereas mutating the first start codon had no effect on the infectivity in plants, the second start codon proved to be essential.
    Keywords: Geminivirus ; Begomovirus ; Ac4 ; Fission Yeast ; Confocal Laser Scanning Microscopy ; Freeze Fracture Immunolabelling ; Virulence ; Biology
    ISSN: 0042-6822
    E-ISSN: 1096-0341
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  • 4
    Language: English
    In: Virology, August, 2014, Vol.462-463, p.189(10)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.virol.2014.06.002 Byline: Katharina Hipp, Peter Rau, Benjamin Schafer, Bruno Gronenborn, Holger Jeske Abstract: Geminiviruses, single-stranded DNA plant viruses, encode a replication-initiator protein (Rep) that is indispensable for virus replication. A potential cyclin interaction motif (RXL) in the sequence of African cassava mosaic virus Rep may be an alternative link to cell cycle controls to the known interaction with plant homologs of retinoblastoma protein (pRBR). Mutation of this motif abrogated rereplication in fission yeast induced by expression of wildtype Rep suggesting that Rep interacts via its RXL motif with one or several yeast proteins. The RXL motif is essential for viral infection of Nicotiana benthamiana plants, since mutation of this motif in infectious clones prevented any symptomatic infection. The cell-cycle link (Clink) protein of a nanovirus (faba bean necrotic yellows virus) was investigated that activates the cell cycle by binding via its LXCXE motif to pRBR. Expression of wildtype Clink and a Clink mutant deficient in pRBR-binding did not trigger rereplication in fission yeast. Author Affiliation: (a) Institut fur Biomaterialien und biomolekulare Systeme, Abteilung fur Molekularbiologie und Virologie der Pflanzen, Universitat Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany (b) Institut des Sciences du Vegetal, CNRS, 91198 Gif-sur-Yvette, France
    Keywords: Virus Diseases -- Health Aspects ; Plants (Organisms) -- Health Aspects ; Proteins -- Health Aspects ; Dna -- Health Aspects
    ISSN: 0042-6822
    Source: Cengage Learning, Inc.
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  • 5
    Language: English
    In: Virology, 15 November 2016, Vol.498
    Description: Plant infecting geminiviruses encode a small (A)C4 protein within the open reading frame of the replication-initiator protein. In African cassava mosaic virus, two in-frame start codons may be used for the translation of a longer and a shorter AC4 variant. Both were fused to green fluorescent protein or glutathione-S-transferase genes and expressed in fission yeast. The longer variant accumulated in discrete spots in the cytoplasm, whereas the shorter variant localized to the plasma membrane. A similar expression pattern was found in plants. A myristoylation motif may promote a targeting of the shorter variant to the plasma membrane. Mass spectrometry analysis of the yeast-expressed shorter variant detected the corresponding myristoylation. The biological relevance of the second start codon was confirmed using mutated infectious clones. Whereas mutating the first start codon had no effect on the infectivity in Nicotiana benthamiana plants, the second start codon proved to be essential. -- Highlights: •The ACMV AC4 may be translated from one or the other in-frame start codon. •Both AC4 variants are translated in fission yeast. •The long AC4 protein localizes to the cytoplasm, the short to the plasma membrane. •The short variant is myristoylated in yeast and may promote membrane localization. •Only the shorter AC4 variant has an impact on viral infections in plants.
    Keywords: 60 Applied LIFE Sciences ; Cassava ; Codons ; Cytoplasm ; Fluorescence ; Genes ; Glutathione ; Infectivity ; Mass Spectroscopy ; Microscopy ; Nicotiana ; Transferases ; Virulence ; Viruses ; Yeasts ; Biology
    ISSN: 0042-6822
    E-ISSN: 1096-0341
    Source: SciTech Connect (U.S. Dept. of Energy - Office of Scientific and Technical Information)
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  • 6
    Language: English
    In: Advances in protein chemistry and structural biology, 2010, Vol.81, pp.61-88
    Description: Electron microscopy together with single-particle image processing is an excellent method for structure determination of biological assemblies that exist in multiple identical copies. Typical assemblies contain several proteins and/or nucleic acids in a defined and reproducible arrangement. Coherent averaging of electron microscopic images of 5000-100,000 copies of these assemblies allows the determination of three-dimensional structures at ca. 1-3-nm resolution. At this intermediate resolution, it is possible to map individual subunits and thus to understand the architecture and quaternary structure of the assemblies. The intermediate resolution structural information gives a solid basis on which pseudo-atomic models of the assemblies can be modeled provided that high-resolution structures of smaller entities are known. The architecture of the assemblies, their pseudo-atomic models, and knowledge on their plasticity during function give a comprehensive understanding of large-scale structural dynamics of multicopy biological complexes. In this review, we will introduce the experimental pipeline and discuss selected examples.
    Keywords: Protein Conformation ; Image Processing, Computer-Assisted -- Methods
    E-ISSN: 1876-1631
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 7
    In: Viruses, 2016, Vol.8(7)
    Description: The capsid proteins (CPs) of geminiviruses combine multiple functions for packaging the single-stranded viral genome, insect transmission and shuttling between the nucleus and the cytoplasm. African cassava mosaic virus (ACMV) CP was expressed in fission yeast, and purified by SDS gel electrophoresis. After tryptic digestion of this protein, mass spectrometry covered 85% of the amino acid sequence and detected three N-terminal phosphorylation sites (threonine 12, serines 25 and 62). Differential centrifugation of cell extracts separated the CP into two fractions, the supernatant and pellet. Upon isopycnic centrifugation of the supernatant, most of the CP accumulated at densities typical for free proteins, whereas the CP in the pellet fraction showed a partial binding to nucleic acids. Size-exclusion chromatography of the supernatant CP indicated high order complexes. In DNA binding assays, supernatant CP accelerated the migration of ssDNA in agarose gels, which is a first hint for particle formation. Correspondingly, CP shifted ssDNA to the expected densities of virus particles upon isopycnic centrifugation. Nevertheless, electron microscopy did not reveal any twin particles, which are characteristic for geminiviruses.
    Keywords: Article ; Geminivirus ; Capsid Protein ; Cp ; Fission Yeast ; Ectopic Expression ; Dna Binding Assay
    E-ISSN: 1999-4915
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  • 8
    Language: English
    In: Frontiers in Microbiology, Jan 7, 2019
    Description: The term “virosphere” describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).
    Keywords: Electron Microscopy -- Usage ; Virus Diseases -- Research ; Virus Diseases -- Diagnosis
    ISSN: 1664-302X
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  • 9
    Language: English
    In: Virology, August 2014, Vol.462-463, pp.189-198
    Description: Geminiviruses, single-stranded DNA plant viruses, encode a replication-initiator protein (Rep) that is indispensable for virus replication. A potential cyclin interaction motif (RXL) in the sequence of African cassava mosaic virus Rep may be an alternative link to cell cycle controls to the known interaction with plant homologs of retinoblastoma protein (pRBR). Mutation of this motif abrogated rereplication in fission yeast induced by expression of wildtype Rep suggesting that Rep interacts via its RXL motif with one or several yeast proteins. The RXL motif is essential for viral infection of plants, since mutation of this motif in infectious clones prevented any symptomatic infection. The cell-cycle link (Clink) protein of a nanovirus (faba bean necrotic yellows virus) was investigated that activates the cell cycle by binding via its LXCXE motif to pRBR. Expression of wildtype Clink and a Clink mutant deficient in pRBR-binding did not trigger rereplication in fission yeast.
    Keywords: Geminivirus ; Rep ; Ac1 ; Rxl Motif ; S. Pombe ; Cell Cycle ; Nanovirus ; Clink ; Biology
    ISSN: 0042-6822
    E-ISSN: 1096-0341
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  • 10
    Language: English
    In: Nucleic acids research, April 2012, Vol.40(7), pp.3275-88
    Description: Ribonuclease P (RNase P) and RNase MRP are closely related ribonucleoprotein enzymes, which process RNA substrates including tRNA precursors for RNase P and 5.8 S rRNA precursors, as well as some mRNAs, for RNase MRP. The structures of RNase P and RNase MRP have not yet been solved, so it is unclear how the proteins contribute to the structure of the complexes and how substrate specificity is determined. Using electron microscopy and image processing we show that eukaryotic RNase P and RNase MRP have a modular architecture, where proteins stabilize the RNA fold and contribute to cavities, channels and chambers between the modules. Such features are located at strategic positions for substrate recognition by shape and coordination of the cleaved-off sequence. These are also the sites of greatest difference between RNase P and RNase MRP, highlighting the importance of the adaptation of this region to the different substrates.
    Keywords: Endoribonucleases -- Chemistry ; Ribonuclease P -- Chemistry
    ISSN: 03051048
    E-ISSN: 1362-4962
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