Download or read book Enabling Evolution with Expanded Genetic Codes written by Drew Scott Tack and published by . This book was released on 2016 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: The natural genetic code is largely shared amongst all terrestrial life, though variations do exist that provide evidence of genetic code evolution. The field of synthetic biology has developed methods to augment and modify the genetic code, by reassigning codons and genetically incorporating noncanonical amino acids (NCAAs). Most commonly, amino-acyl tRNA synthetases and their cognate tRNAs are engineered to recognize (NCAAs), the tRNA charged with an NCAA is then used during translation to decode the amber stop codon. Using this method, over 200 unique NCAAs have been added to the genetic code, allowing for the site-specific incorporation of useful chemistries, including covalent bond formation and fluorescence. NCAAs have been implemented in biological research and protein engineering. The second chapter of this dissertation explores the biophysical parameters that allow efficient crosslinking with a NCAA. We investigated several environmental factors which could impact crosslinking between two interacting proteins. We define a set of parameters that permit efficient crosslinking. Noncanonical amino acids are a potentially powerful tool in understanding genetic code evolution. Evolutionary experiments using NCAAs have already been used to explore proposed theories on codon evolution, including codon capture and ambiguous intermediate theories. Though several studies have explored the implications of NCAAs in evolution, significant obstacles have prevented the long-term evolution of wild-type organisms with expanded genetic codes. In chapter three of this dissertation we demonstrate that a single essential enzyme can be engineered to be structurally dependent on a genetically encoded NCAA. This confers a functional addiction to the NCAA and the addiction can be transferred to new bacterial hosts using a DNA plasmid. Chapter four expands on this idea, attempting to use the chemistries bestowed by the NCAA for active site chemistry. Finally, in chapter five we demonstrate that a protein-conferred cellular NCAA addiction is sufficient for the long-term evolution of bacteria with a recoded amber codon. We investigated the genetic and phenotypic impact of evolution with an expanded genetic code.
Download or read book Directed Evolution of and with Expanded Genetic Codes written by Chang C. Liu and published by . This book was released on 2009 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: By expanding the genetic code to allow the cotranslational incorporation of unnatural amino acids, one can site-specifically introduce unique chemical functionality into proteins in vivo. By using such expanded genetic codes in directed evolution, one can impose selection for novel protein function wherein variants containing unnatural amino acids will be selected should the unnatural amino acids confer a functional advantage. I first describe the expansion of E. coli 's genetic code for the site-specific incorporation of the unnatural amino acid sulfotyrosine and the subsequent use of this expanded genetic code for the expression and study of several proteins including sulfo-hirudin and sulfated anti-HIV antibodies. I then describe the development of a phage-based system for evolution with expanded genetic codes and the application of this system for directed evolution, through which proteins that use unnatural amino acids for enhanced function can emerge from selection. This work demonstrates the value of genetically encoding more than the 20 natural amino acids for protein engineering applications and shows that these expanded genetic codes can confer a selective advantage.
Download or read book Evolution of the Genetic Code written by Shōzō Ōsawa and published by . This book was released on 1995 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genetic code was deciphered experimentally around 1966 and for a number of years scientists considered it to be "universal" for all forms of life. In 1981 researchers shocked the scientific community with the discovery that the code differed in mitochondria and certain other organisms, evidence that the genetic code was still evolving. This book discusses the distribution and origin of the non-universal codes and examines the possible mechanisms of code changes, making it essential reading for all those interested in evolutionary genetics.
Download or read book Synthetic DNA and RNA Programming written by Patrick O’Donoghue and published by MDPI. This book was released on 2019-11-19 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dear Colleagues, Synthetic biology is a broad and emerging discipline that capitalizes on recent advances in molecular biology, genetics, protein and RNA engineering and omics technologies. These technologies have transformed our ability to reveal the biology of the cell and the molecular basis of disease. This Special Issue on “Synthetic RNA and DNA Programming” features original research articles and reviews, highlighting novel aspects of basic molecular biology and the molecular mechanisms of disease that were uncovered by the application and development of novel synthetic biology-driven approaches.
Download or read book Non Natural Amino Acids written by and published by Academic Press. This book was released on 2009-07-24 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: By combining the tools of organic chemistry with those of physical biochemistry and cell biology, Non-Natural Amino Acids aims to provide fundamental insights into how proteins work within the context of complex biological systems of biomedical interest. The critically acclaimed laboratory standard for 40 years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. With more than 400 volumes published, each Methods in Enzymology volume presents material that is relevant in today's labs -- truly an essential publication for researchers in all fields of life sciences. - Demonstrates how the tools and principles of chemistry combined with the molecules and processes of living cells can be combined to create molecules with new properties and functions found neither in nature nor in the test tube - Presents new insights into the molecular mechanisms of complex biological and chemical systems that can be gained by studying the structure and function of non-natural molecules - Provides a "one-stop shop" for tried and tested essential techniques, eliminating the need to wade through untested or unreliable methods
Download or read book The Impact of Synthetically Expanded Genetic Codes on Evolvability written by Michael J. Hammerling and published by . This book was released on 2016 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic biology allows researchers to address previously unanswerable biological questions through the wholesale reengineering of living systems. Even one of the most fundamental properties of biology – the canonical genetic code for the translation of genetic information into proteins – may now be altered to include nonstandard amino acids (nsAAs) because synthetic incorporation systems for nsAAs now match native host machinery in terms of efficiency and fidelity. However, the evolutionary stability of these systems and the potential for them to promote the evolvability of the organisms in which they are deployed remains mostly unexplored. In chapter one of this dissertation, I explore how Escherichia coli strains that incorporate a 21st nsAA at the recoded amber (TAG) stop codon evolve resistance to the antibiotic rifampicin. I found a variety of mutations that lead to substitutions of nsAAs in the essential RpoB protein confer robust rifampicin resistance, and I interpret these results in a framework in which an expanded code can increase evolvability in two distinct ways. I consider the implications of these results for the evolution of alternative genetic codes, in particular their support for the codon capture model of genetic code evolution. In chapters 2 and 3, I employ bacteriophage T7, which utilizes the translation apparatus of its E. coli host, as a model organism for whole-genome evolution with an expanded genetic code. I show that phages evolved on an E. coli host that incorporates 3-iodotyrosine became dependent on an alternative genetic code as they adapted to higher fitness. In particular, phages with a 3-iodotyrosine substitution in the type II holin protein outcompete phages with canonical amino acids at this position. Inspired by this surprising outcome, I performed massively parallel evolution experiments in T7 with six expanded genetic codes, finding over a thousand substitutions to nsAAs in these experiments, many of which displayed genomic signatures of positive selection. Two of the nsAAs accumulated in genomes at a rate comparable to a mock genetic code expansion with the canonical amino acid tyrosine. Together these results show that expanded genetic codes alter functional sequence space and create new possibilities for adaptive mutations, thereby improving evolvability in these organisms.
Download or read book Applications of an Expanded Genetic Code written by Eric M. Brustad and published by ProQuest. This book was released on 2008 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: With an ever expanding genetic code it is no longer a question of whether an unnatural amino acid can be introduced into a protein sequence, but what can be done with them. This thesis describes the introduction of novel amino acids to the genetic codes of E. coli and yeast and the applications of those amino acids towards novel protein biochemistry and the study of biomolecular structure and function. This includes the development of orthogonal protein labeling strategies that allow the site-specific attachment of biophysical probes and other molecules onto a protein surface. An unnatural ketone containing amino acid is described that allows the general and efficient introduction of fluorophores and spin probes onto a protein surface. This chemistry is exploited for the site-specific double labeling of proteins with fluorophores and the utility of this methodology is demonstrated by the examination of bacteriophage T4 lysozyme folding via single molecule fluorescence energy transfer. To expand the orthogonal chemistry presented by unnatural amino acid mutagenesis, the addition of a boronic acid containing amino acid to the genetic code of E. coli is also described. The unique chemistry of this functionality is exploited for the site-specific labeling of proteins with fluorophores through Suzuki coupling reactions as well as the formation boronic esters with diol containing compounds. This latter chemistry is also useful for the genetic encoding of carbohydrate recognition into a protein sequence as well as the development of a single step scarless protein purification methodology. The evolution of the E. coli leucyl tRNA synthetase for the site-selective introduction of methionine, cysteine and alanine analogs into proteins in yeast is also described. From this work, a single tRNA synthetase that shows promiscuous activity for over ten unnatural amino acid structures is investigated. Finally, a project investigating the role and source of reactive oxygen species in cytokine signaling is also be briefly discussed.
Download or read book Engineering the Genetic Code written by Nediljko Budisa and published by John Wiley & Sons. This book was released on 2006-05-12 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to introduce non-canonical amino acids in vivo has greatly expanded the repertoire of accessible proteins for basic research and biotechnological application. Here, the different methods and strategies to incorporate new or modified amino acids are explained in detail, including a lot of practical advice for first-time users of this powerful technique. Novel applications in protein biochemistry, genomics, biotechnology and biomedicine made possible by the expansion of the genetic code are discussed and numerous examples are given. Essential reading for all molecular life scientists who want to stay ahead in their research.
Download or read book Sequence Evolution Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Selfish Gene written by Richard Dawkins and published by Oxford University Press, USA. This book was released on 1989 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Science need not be dull and bogged down by jargon, as Richard Dawkins proves in this entertaining look at evolution. The themes he takes up are the concepts of altruistic and selfish behaviour; the genetical definition of selfish interest; the evolution of aggressive behaviour; kinshiptheory; sex ratio theory; reciprocal altruism; deceit; and the natural selection of sex differences. 'Should be read, can be read by almost anyone. It describes with great skill a new face of the theory of evolution.' W.D. Hamilton, Science
Download or read book The Origin and Evolution of the Genetic Code 100th Anniversary Year of the Birth of Francis Crick written by Koji Tamura and published by MDPI. This book was released on 2018-03-23 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "The Origin and Evolution of the Genetic Code: 100th Anniversary Year of the Birth of Francis Crick" that was published in Life
Download or read book The Extended Phenotype written by Richard Dawkins and published by Oxford University Press. This book was released on 2016 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: In The Selfish Gene, Richard Dawkins crystallized the gene's eye view of evolution developed by W.D. Hamilton and others. The book provoked widespread and heated debate. Written in part as a response, The Extended Phenotype gave a deeper clarification of the central concept of the gene as the unit of selection; but it did much more besides. In it, Dawkins extended the gene's eye view to argue that the genes that sit within an organism have an influence that reaches out beyond the visible traits in that body - the phenotype - to the wider environment, which can include other individuals. So, for instance, the genes of the beaver drive it to gather twigs to produce the substantial physical structure of a dam; and the genes of the cuckoo chick produce effects that manipulate the behaviour of the host bird, making it nurture the intruder as one of its own. This notion of the extended phenotype has proved to be highly influential in the way we understand evolution and the natural world. It represents a key scientific contribution to evolutionary biology, and it continues to play an important role in research in the life sciences. The Extended Phenotype is a conceptually deep book that forms important reading for biologists and students. But Dawkins' clear exposition is accessible to all who are prepared to put in a little effort. Oxford Landmark Science books are 'must-read' classics of modern science writing which have crystallized big ideas, and shaped the way we think.
Download or read book Noncanonical Amino Acids written by Edward A. Lemke and published by . This book was released on 2018 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Advances in Synthetic Biology written by Vijai Singh and published by Springer Nature. This book was released on 2020-04-13 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses the design of emerging conceptual tools, technologies and systems including novel synthetic parts, devices, circuits, oscillators, biological gates, and small regulatory RNAs (riboregulators and riboswitches), which serve as versatile control elements for regulating gene expression. Synthetic biology, a rapidly growing field that involves the application of engineering principles in biology, is now being used to develop novel systems for a wide range of applications including diagnostics, cell reprogramming, therapeutics, enzymes, vaccines, biomaterials, biofuels, fine chemicals and many more. The book subsequently summarizes recent developments in technologies for assembling synthetic genomes, minimal genomes, synthetic biology toolboxes, CRISPR-Cas systems, cell-free protein synthesis systems and microfluidics. Accordingly, it offers a valuable resource not only for beginners in synthetic biology, but also for researchers, students, scientists, clinicians, stakeholders and policymakers interested in the potential held by synthetic biology.
Download or read book Recoding Expansion of Decoding Rules Enriches Gene Expression written by John F. Atkins and published by Springer Science & Business Media. This book was released on 2010-03-10 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10–13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA.
Download or read book TRNA written by Dieter Söll and published by . This book was released on 1995 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt:
