Author: Johannes Jacobus van den Heuvel
Publisher:
ISBN:
Category :
Languages : en
Pages : 80

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Author: Caitlin E. Gamble
Publisher:
ISBN:
Category :
Languages : en
Pages : 124

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Synonymous codon choice modulates translation, but the properties of codons or codon combinations that result in impaired translation are not understood. We scored expression of 35,811 three-codon insertions in GFP in Saccharomyces cerevisiae and evaluated these variants for codon usage and RNA structure effects on GFP fluorescence levels. We have established that codon pairs affect translation elongation and efficiency in yeast in a manner distinct from the effects of individual codon tRNA abundance. Also, similar to previous studies in bacteria, we have found that the base-pairing status of nucleotides near the translation start site is likely to impair translation initiation. Both inhibitory codon pairs and 5’ mRNA structure can impose substantial limitations on translation efficiency through synonymous variation. For 17 inhibitory codon pairs, we show that it is the pair, rather than the dipeptide, the 6-base sequence, or the two individual codons, that is responsible for inhibition. Variants from the GFP insertion library that had an inhibitory pair had significantly lower expression than variants in which: the 6 base sequences were out of frame; the two codons were present but separated; or one of the codons of the pair was instead an optimal codon. We find that the inhibitory pairs act in translation, based on both suppression of inhibition by over expressed tRNA (11/12 tested) and the reduction in translation speeds relative to synonymous dipeptide sequences, as observed from ribosome occupancies along yeast transcripts. Furthermore, for 12 of the 17 pairs, preserving the order of codons in the pair was required for strong inhibitory effects. Thus the position of inhibitory pairs within the ribosome is likely a key factor in translation efficiency. Moreover, the identity of codons in inhibitory pairs is inconsistent with an inhibition mechanism governed primarily by limited tRNA supply. Rather, our data implicates wobble decoding and interactions between adjacent sites in the ribosome. The high-throughput experimental analysis described here has resulted in the direct and extensive identification of multiple inhibitory codon pairs, a quantitative analysis of their relative effects on translation in vivo, and tests of their activity as modulators of translation.

Author:
Publisher:
ISBN: 9780815332183
Category : Cells
Languages : en
Pages : 0

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Author: Christina Waldsich
Publisher: Humana
ISBN: 9781493960583
Category : Medical
Languages : en
Pages : 0

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Focusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.

Author: Peter Zwickl
Publisher: Springer Science & Business Media
ISBN: 364259414X
Category : Science
Languages : en
Pages : 222

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Book Description
This volume gives an overview of pro tea some-mediated protein degradation and the regulatory role of the ubiquitin system in cellular proteolysis. The first chapter describes the molecular evolution of the proteasome and its associated activators, i. e. , the 20S core, the base and the lid of the 19S cap, and the 11 S regulator. The ensuing chapter gives an overview of the structure and assembly of the 20S proteasome and the regulation of the archaeal proteasome by PAN. The third contribution summarizes our knowledge on the eukaryotic 26S proteasome and its regulation by the 19S regu lator, followed by a chapter devoted to the llS regulator, which elucidates the structural basis for the 11 S-mediated activation of the 20S proteasome. The fifth chapter reviews in detail the role of the proteasome in the immune response. The subsequent chapter of the natural substrates of the gives a comprehensive description proteasome and their recognition by the enzymes of the ubiqui tination machinery. The penultimate chapter rounds up the in formation on intracellular distribution of proteasomes in yeast and mammalian cells, while the last contribution highlights proteasome inhibitors, tools which proved to be very valuable for dissecting the cellular roles of the proteasome and which might turn out to be of pharmacological importance.

Author: Nahum Sonenberg
Publisher: CSHL Press
ISBN: 9780879696184
Category : Gene expression
Languages : en
Pages : 1034

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Book Description
Since the 1996 publication of Translational Control, there has been fresh interest in protein synthesis and recognition of the key role of translation control mechanisms in regulating gene expression. This new monograph updates and expands the scope of the earlier book but it also takes a fresh look at the field. In a new format, the first eight chapters provide broad overviews, while each of the additional twenty-eight has a focus on a research topic of more specific interest. The result is a thoroughly up-to-date account of initiation, elongation, and termination of translation, control mechanisms in development in response to extracellular stimuli, and the effects on the translation machinery of virus infection and disease. This book is essential reading for students entering the field and an invaluable resource for investigators of gene expression and its control.

Author: Jens Nielsen
Publisher: Springer
ISBN: 3540453008
Category : Science
Languages : en
Pages : 193

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Book Description
Metabolic engineering is a rapidly evolving field that is being applied for the optimization of many different industrial processes. In this issue of Advances in Biochemical Engineering/Biotechnology, developments in different areas of metabolic engineering are reviewed. The contributions discuss the application of metabolic engineering in the improvement of yield and productivity - illustrated by amino acid production and the production of novel compounds - in the production of polyketides and extension of the substrate range - and in the engineering of S. cerevisiae for xylose metabolism, and the improvement of a complex biotransformation process.

Author: Shona L. Innes
Publisher:
ISBN:
Category :
Languages : en
Pages : 502

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Author: Richard H. Baltz
Publisher: ASM Press
ISBN:
Category : Science
Languages : en
Pages : 320

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Book Description
This book is based on the proceedings of the 5th ASM Conference on the Genetics and Molecular Biology of Industrial Microorganisms held in Bloomington, Indiana in October 1992. The meeting focussed on prokaryotes and lower eukaryotes, with the programme balanced between streptomyces, fungi and yeasts, and other bacteria including Escherichia coli and emerging bacterial systems. The topics of the symposia reflect major trends in research that have immediate and future industrial applications

Author: Christine Guthrie
Publisher:
ISBN: 9780123106704
Category : Molecular biology
Languages : en
Pages : 933

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Book Description
Guide to Yeast Genetics and Molecular Biology presents, for the first time, a comprehensive compilation of the protocols and procedures that have made Saccharomyces cerevisiae such a facile system for all researchers in molecular and cell biology. Whether you are an established yeast biologist or a newcomer to the field, this volume contains all the up-to-date methods you will need to study "Your Favorite Gene" in yeast. Basic Methods in Yeast Genetics**Physical and genetic mapping**Making and recovering mutants**Cloning and Recombinant DNA Methods**High-efficiency transformation**Preparation of yeast artificial chromosome vectors**Basic Methods of Cell Biology**Immunomicroscopy**Protein targeting assays**Biochemistry of Gene Expression**Vectors for regulated expression**Isolation of labeled and unlabeled DNA, RNA, and protein