Evolutionary Relationships, Design, and Biochemical Characterization of Homing Endonucleases - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Evolutionary Relationships, Design, and Biochemical Characterization of Homing Endonucleases write by Gregory K. Taylor. This book was released on 2011. Evolutionary Relationships, Design, and Biochemical Characterization of Homing Endonucleases available in PDF, EPUB and Kindle. Homing endonucleases, found in all forms of microbial life, facilitate the invasion of host genes often in concert with introns or inteins by generating double stranded breaks in conserved coding sequences. There are five homing endonuclease families distinct in their structural characteristics and each family appears to share a common ancestor with diverse host proteins of unrelated function. Such related proteins include restriction endonucleases, DNA mismatch repair proteins, transcription factors, four-way junction resolving enzymes, and colicins. Homing endonculeases are currently being computationally redesigned for applications in genome engineering and structures of three redesigned homing endonuclease variants are described. In these experiments, crystal structures uncovered unexpected shifts in the DNA backbone relative to the wild type endonucleases and have thus been informative in the redesign process. Recently, a sixth homing endonuclease family homologous to E. Coli DNA repair protein VSR was discovered. A series of biochemical and x-ray crystallographic experiments investigating binding specificity and catalytic mechanism of a representative family member I-Bth0305I are described. Finally, a database archiving experimentally characterized homing endonucleases and a web-base program supporting homing endonuclease target site search are discussed.
An Evolutionary and Biochemical Characterization of a Self-splicing Group II Intron and Its Encoded LAGLIDADG Homing Endonuclease in Leptographium Truncatum
An Evolutionary and Biochemical Characterization of a Self-splicing Group II Intron and Its Encoded LAGLIDADG Homing Endonuclease in Leptographium Truncatum - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook An Evolutionary and Biochemical Characterization of a Self-splicing Group II Intron and Its Encoded LAGLIDADG Homing Endonuclease in Leptographium Truncatum write by Sahra-Taylor Mullineux. This book was released on 2010. An Evolutionary and Biochemical Characterization of a Self-splicing Group II Intron and Its Encoded LAGLIDADG Homing Endonuclease in Leptographium Truncatum available in PDF, EPUB and Kindle. Evolutionary relationships amongst strains of the fungal genus Leptographium and related taxa were inferred using the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA repeat. To generate robust sequence alignments for phylogenetic analysis the relationship between DNA sequence variability and RNA structural conservation of ITS segments was examined. The results demonstrate that structural conservation of helical regions is facilitated by compensatory base changes, compensating insertions/deletions, and, possibly, RNA strand slippage. A high mol % G+C bias for ITS1 and ITS2 and structural constraints at the RNA level appear to limit the types of changes observed. Fifty strains of Leptographium were screened for the presence of introns within mitochondrial genes. Superimposing intron survey data onto the ITS-derived phylogenetic tree reveals that introns are absent from the small ribosomal RNA (rns) gene of all strains of L. procerum yet are found in all strains of L. lundbergii. Amongst members of L. wingfieldii, L. terebrantis, and L. truncatum intron distribution is stochastic and is not correlated to the evolutionary relationships amongst strains. A group II intron/LAGLIDADG homing endonuclease gene (HEG) composite element from the mt rns gene of L. truncatum strain CBS929.85 was characterized. Intron-catalyzed splicing was tested using ORF-less and ORF-containing precursor transcripts, and both versions of the intron readily self-splice under moderate temperature and ionic conditions (37 °C and 6 mM MgCl2). Cleavage activity of the intron-encoded protein (I-LtrII) was tested using an N-terminal His6-tagged and near native protein. The homing endonuclease cleaves double-stranded DNA 2 nucleotides upstream of the intron insertion site within the exon, generating 4 nucleotide 3' OH overhangs. Intron splicing is not enhanced by the addition of I-LtrII and RNA-binding assays indicate that the His6-tagged protein does not bind to the intron. Phylogenetic relationships amongst the rns gene, intron, and amino acid sequences were inferred. An evolutionary model of the composite element is proposed in which the HEG invaded a group II intron and mobilized it. The mobile genetic element may be transmitted vertically amongst L. lundbergii strains and horizontally through lateral gene transfer amongst strains of L. wingfieldii, L. terebrantis, and L. truncatum.
Homing Endonucleases and Inteins
Homing Endonucleases and Inteins - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Homing Endonucleases and Inteins write by Marlene Belfort. This book was released on 2005-12-29. Homing Endonucleases and Inteins available in PDF, EPUB and Kindle. This book provides the first and only comprehensive description and detailed summary of the genetics, structure, function, mechanisms of action, evolution and engineering of homing endonucleases and inteins. These two unique protein superfamilies, which are tied together through their frequent fusion and coevolution, have generated considerable excitement for their fundamental, structural, and functional properties, their evolution as parasitic elements, and their widespread applications as gene targeting agents and as instruments for the generation of modified proteins and novel protein combinations.
Mitochondria and Anaerobic Energy Metabolism in Eukaryotes
Mitochondria and Anaerobic Energy Metabolism in Eukaryotes - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Mitochondria and Anaerobic Energy Metabolism in Eukaryotes write by William F. Martin. This book was released on 2020-12-07. Mitochondria and Anaerobic Energy Metabolism in Eukaryotes available in PDF, EPUB and Kindle. Mitochondria are sometimes called the powerhouses of eukaryotic cells, because mitochondria are the site of ATP synthesis in the cell. ATP is the universal energy currency, it provides the power that runs all other life processes. Humans need oxygen to survive because of ATP synthesis in mitochondria. The sugars from our diet are converted to carbon dioxide in mitochondria in a process that requires oxygen. Just like a fire needs oxygen to burn, our mitochondria need oxygen to make ATP. From textbooks and popular literature one can easily get the impression that all mitochondria require oxygen. But that is not the case. There are many groups of organismsm known that make ATP in mitochondria without the help of oxygen. They have preserved biochemical relicts from the early evolution of eukaryotic cells, which took place during times in Earth history when there was hardly any oxygen avaiable, certainly not enough to breathe. How the anaerobic forms of mitochondria work, in which organisms they occur, and how the eukaryotic anaerobes that possess them fit into the larger picture of rising atmospheric oxygen during Earth history are the topic of this book.
Restriction Endonucleases
Restriction Endonucleases - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Restriction Endonucleases write by Alfred Pingoud. This book was released on 2012-12-06. Restriction Endonucleases available in PDF, EPUB and Kindle. Restriction enzymes are highly specific nucleases which occur ubiquitously among prokaryotic organisms, where they serve to protect bacterial cells against foreign DNA. Many different types of restriction enzymes are known, among them multi-subunit enzymes which depend on ATP or GTP hydrolysis for target site location. The best known representatives, the orthodox type II restriction endonucleases, are homodimers which recognize palindromic sequences, 4 to 8 base pairs in length, and cleave the DNA within or immediately adjacent to the recognition site. In addition to their important biological role (up to 10 % of the genomes of prokaryotic organisms code for restriction/modification systems!), they are among the most important enzymes used for the analysis and recombination of DNA. In addition, they are model systems for the study of protein-nucleic acids interactions and, because of their ubiquitous occurence, also for the understanding of the mechanisms of evolution.
