| 1. |
- Esberg, Anders, et al.
(författare)
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Elevated levels of two tRNA species bypass the requirement for elongator complex in transcription and exocytosis.
- 2006
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Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765 .- 1097-4164. ; 24:1, s. 139-148
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Tidskriftsartikel (refereegranskat)abstract
- The Saccharomyces cerevisiae Elongator complex consisting of the six Elp1-Elp6 proteins has been proposed to participate in three distinct cellular processes: transcriptional elongation, polarized exocytosis, and formation of modified wobble uridines in tRNA. Therefore it was important to clarify whether Elongator has three distinct functions or whether it regulates one key process that leads to multiple downstream effects. Here, we show that the phenotypes of Elongator-deficient cells linking the complex to transcription and exocytosis are suppressed by increased expression of two tRNA species. Elongator is required for formation of the mcm(5) group of the modified wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U) in these tRNAs. Hence, in cells with normal levels of these tRNAs, presence of mcm(5)s(2)U is crucial for posttranscriptional expression of gene products important in transcription and exocytosis. Our results indicate that the physiologically relevant function of the evolutionary-conserved Elongator complex is in formation of modified nucleosides in tRNAs.
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| 2. |
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| 3. |
- He, Feng, et al.
(författare)
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Chapter 6. Qualitative and quantitative assessment of the activity of the yeast nonsense-mediated mRNA decay pathway.
- 2008
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Ingår i: Methods in Enzymology. - 0076-6879 .- 1557-7988. ; 449, s. 127-47
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Tidskriftsartikel (refereegranskat)abstract
- The yeast Saccharomyces cerevisiae provides an ideal model system for elucidation of the molecular mechanisms that regulate the nonsense-mediated mRNA decay (NMD) pathway. This chapter describes an array of molecular biological, genetic, and biochemical tools that facilitate the characterization of transcripts that comprise NMD substrates and provide insights into the roles of the upf/nmd proteins in mRNA decay and translation termination. Examples illustrate the use of these methods in wild-type and NMD-deficient cells to monitor the abundance, structure, and half-lives of nonsense-containing mRNAs, the read through of premature termination codons by the ribosome, and the positioning of ribosomes at or near normal and premature termination codons.
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| 4. |
- Huang, Bo, et al.
(författare)
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An early step in wobble uridine tRNA modification requires the Elongator complex
- 2005
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Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 11:4, s. 424-436
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Tidskriftsartikel (refereegranskat)abstract
- Elongator has been reported to be a histone acetyltransferase complex involved in elongation of RNA polymerase II transcription. In Saccharomyces cerevisiae, mutations in any of the six Elongator protein subunit (ELP1–ELP6) genes or the three killer toxin insensitivity (KTI11–KTI13) genes cause similar pleiotropic phenotypes. By analyzing modified nucleosides in individual tRNA species, we show that the ELP1–ELP6 and KTI11–KTI13 genes are all required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA. Transfer RNA immunoprecipitation experiments showed that the Elp1 and Elp3 proteins specifically coprecipitate a tRNA susceptible to formation of an mcm5 side chain, indicating a direct role of Elongator in tRNA modification. The presence of mcm5U, ncm5U, or derivatives thereof at the wobble position is required for accurate and efficient translation, suggesting that the phenotypes of elp1–elp6 and kti11–kti13 mutants could be caused by a translational defect. Accordingly, a deletion of any ELP1–ELP6 or KTI11–KTI13 gene prevents an ochre suppressor tRNA that normally contains mcm5U from reading ochre stop codons.
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| 5. |
- Johansson, Bengt J O, 1948
(författare)
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Betong i arkitekturen. Gestaltning och teknik 1930-1980
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Bengt J O Johansson: Betong i arkitekturen. Gestaltning och teknik 1930–1980 (Concrete in Architecture. Design and Technology 1930–1980). Göteborg 2008.Written in Swedish with an English summary.This is a study of the interaction between design and technology for buildings of concrete construction during 1930-1980. Its aim is to describe the design and constructional development during the different stages of style change throughout this period, and how design and technology have influenced each other. Knowledge about building technology utilising concrete is essential for understanding the building heritage of our own era.The study encompasses architecture and construction technology. The sources are literature and drawings, and the buildings themselves.The study begins with an account of the development of concrete building technology during the period in question. Construction technology provides the basis for the analysis of the interaction with architecture. This interaction is described in three thematically sectioned chapters and summarised and analysed in a concluding chapter. These thematic chapters deal with concrete as ’the material for modernism’, as ‘the material for design’ and as ‘the material for rationalism’.Concrete construction was at the beginning of the 1930s an ideal in the creation of functionalist (modernistic) architecture, even if the structures were initially mostly of traditional character. During this decennium, however, concrete became the most commonly used material for construction in buildings.From the 1950s onwards, on-site concrete constructions were utilised in the creation of buildings of character. The textured surface of the concrete, often derived by carefully shaped casts or through finishing processes made a vital contribution to the design. Concrete formed load-bearing elements and constructions gave design to interiors, exte-riors, and even complete volumes. Architects adopted concrete construction technology and at the same time freed themselves from traditional architecture with historical roots. This resulted in painstakingly designed concrete buildings.Parallel with this, from the 1960s onwards, industrialised construction with precast concrete modular sections for entire building structures and façades were developed. Here the construction process and prefabrication technology became design-oriented motives, often finding expression through their large-scale, repetition, and duplication of identical modular units in the individual building and the repetition of identical buildings. The concrete surfaces of the façades’ sectional units were produced rationally; they formed and accentuated this industrialised construction.
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| 6. |
- Johansson, Marcus J O, et al.
(författare)
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Association of yeast Upf1p with direct substrates of the NMD pathway.
- 2007
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:52, s. 20872-7
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Tidskriftsartikel (refereegranskat)abstract
- Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that detects and degrades transcripts containing premature translation termination codons. Gene expression profiling experiments have shown that inactivation of the NMD pathway leads to the accumulation of both aberrant, nonsense-containing mRNAs, and many apparently wild-type transcripts. Such increases in transcript steady-state levels could arise from direct changes in the respective mRNA half-lives, or indirectly, as a consequence of the stabilization of transcripts encoding specific regulatory proteins. Here, we distinguished direct from indirect substrates by virtue of their association with the Saccharomyces cerevisiae Upf1 protein. Analyses of this dataset, and its comparison to the sets of transcripts that respectively increase or decrease in abundance when NMD is either inactivated or reactivated, indicate that the number of direct NMD substrates is larger than previously thought and that low abundance, alternatively transcribed mRNAs, i.e., mRNAs whose 5' ends are derived from previously unannotated 5' flanking sequences, comprise a significant class of direct substrates. Using thiamine metabolism as an example, we also show that apparent NMD-regulated cellular pathways may actually reflect the detection of low-abundance alternative transcripts under conditions where a pathway is repressed.
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| 7. |
- Johansson, Marcus J O, et al.
(författare)
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Eukaryotic wobble uridine modifications promote a functionally redundant decoding system.
- 2008
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Ingår i: Molecular and Cellular Biology. - 0270-7306 .- 1098-5549. ; 28:10, s. 3301-3312
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Tidskriftsartikel (refereegranskat)abstract
- The translational decoding properties of tRNAs are modulated by naturally occurring modifications of their nucleosides. Uridines located at the wobble position (nucleoside 34 [U34]) in eukaryotic cytoplasmic tRNAs often harbor a 5-methoxycarbonylmethyl (mcm(5)) or a 5-carbamoylmethyl (ncm(5)) side chain and sometimes an additional 2-thio (s2) or 2'-O-methyl group. Although a variety of models explaining the role of these modifications have been put forth, their in vivo functions have not been defined. In this study, we utilized recently characterized modification-deficient Saccharomyces cerevisiae cells to test the wobble rules in vivo. We show that mcm5 and ncm5 side chains promote decoding of G-ending codons and that concurrent mcm5 and s2 groups improve reading of both A- and G-ending codons. Moreover, the observation that the mcm5U34- and some ncm5U34-containing tRNAs efficiently read G-ending codons challenges the notion that eukaryotes do not use U-G wobbling.
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| 8. |
- Johansson, Marcus J O, et al.
(författare)
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Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae.
- 2005
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Ingår i: Fine-Tuning of RNA Functions by Modification and Editing.. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783540244950 - 9783540314547 ; , s. 87-120
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Bokkapitel (refereegranskat)abstract
- Transfer RNAs are adaptor molecules, which decode mRNA into protein and, thereby, play a central role in gene expression. During the maturation of a primary tRNA transcript, specific subsets of the four normal nucleosides adenosine, cytidine, guanosine, and uridine are modified. The formation of a modified nucleoside can require more than one gene product and may involve several enzymatic steps. In the last few years, the identification of gene products required for formation of modified nucleosides in tRNA has dramatically increased. In this review, proteins involved in modification of cytoplasmic tRNAs in Saccharomyces cerevisiae are described, emphasizing phenotypic characteristics of modification deficient strains and genetic approaches used to determine the in vivo role of modified nucleosides/modifying enzymes.
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| 9. |
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| 10. |
- Korzhavyi, Pavel A., 1966-, et al.
(författare)
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Electronic structure and effective chemical and magnetic exchange interactions in bcc Fe-Cr alloys
- 2009
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 79:5, s. 054202-
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Forskningsöversikt (refereegranskat)abstract
- Electronic structure calculations are employed in order to investigate the cohesive properties (lattice parameter, enthalpy of formation, and bulk modulus) of random Fe-Cr alloys as a function of composition and magnetic state, as well as to derive the chemical and magnetic exchange interactions of the constituent atoms. The calculations predict certain anomalies in the cohesive properties of ferromagnetic alloys at a concentration of about 7 at % Cr; these anomalies may be related to the changes in Fermi-surface topology that occur with composition in this alloy system. The obtained interatomic interactions are used as parameters in the configurational (Ising) and magnetic (Heisenberg) Hamiltonians for modeling finite-temperature thermodynamic properties of the alloys. We discuss the approximations and limitations of similar modeling approaches, investigate the origin of existing difficulties, and analyze possible ways of extending the theoretical models in order to capture the essential physics of interatomic interactions in the Fe-Cr or similar alloys where magnetism plays a crucial role in the phase stability.
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