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The Origin and Evolution of the Genetic Code: 100th Anniversary Year of the Birth of Francis Crick

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ISBN: 9783038427698 9783038427704 Year: Pages: X, 192 DOI: 10.3390/books978-3-03842-770-4 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology --- Genetics
Added to DOAB on : 2018-04-06 13:38:32
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The genetic code is one of the greatest discoveries of the 20th century as it is central to life itself. It is the algorithm that connects 64 RNA triplets to 20 amino acids, thus functioning as the Rosetta Stone of molecular biology. Following the discovery of the structure of DNA by James Watson and Francis Crick in 1953, George Gamow organized the 20-member “RNA Tie Club” to discuss the transmission of information by DNA. Crick, Sydney Brenner, Leslie Barnett, and Richard Watts-Tobin first demonstrated the three bases of DNA code for one amino acid. The decoding of the genetic code was begun by Marshall Nirenberg and Heinrich Matthaei and was completed by Har Gobind Khorana. Then, finally, Brenner, Barnett, Eugene Katz, and Crick placed the last piece of the jigsaw puzzle of life by proving that UGA was a third stop codon. In the mid-1960s, Carl Woese proposed the “stereochemical hypothesis”, which speculated that the genetic code derives from a type of codon–amino acid-pairing interaction. The origin and evolution of the genetic code remains a mystery despite numerous theories and attempts to understand these. In this Special Issue, experts in the field present their thoughts and views on this topic. Because 2016 commemorated the 100th anniversary of the birth of Francis Crick, the Guest Editor of this Special Issue also dedicates all articles included herein to the memory of Francis Crick.

Molecular Biology of the Transfer RNA Revisited

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193660 Year: Pages: 164 DOI: 10.3389/978-2-88919-366-0 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General)
Added to DOAB on : 2015-11-19 16:29:12
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Transfer RNAs (tRNAs) are one of the classical non-coding RNAs whose lengths are approximately 70–100 bases. The secondary structure of tRNAs can be represented as the cloverleaf with 4 stems, and the three dimensional structure as an “L” shape. Historically, the basic function of tRNA as an essential component of translation was established in 1960s, i.e., each tRNA is charged with a target amino acid and these are delivered to the ribosome during protein synthesis. However, recent data suggests that the role of tRNA in cellular regulation goes beyond this paradigm. In most Archaea and Eukarya, precursor tRNAs are often interrupted by a short intron inserted strictly between the first and second nucleotide downstream of the anticodon, known as canonical nucleotide position (37/38). Recently, a number of reports describe novel aspects of tRNAs in terms of gene diversity, for example, several types of disrupted tRNA genes have been reported in the Archaea and primitive Eukarya, including multiple-intron-containing tRNA genes, split tRNA genes, and permuted tRNA genes. Our understanding of the enzymes involved in tRNA functions (e.g., aminoacyl-tRNA synthetase, tRNA splicing endonuclease, tRNA ligase) has deepened. Moreover, it is well known that tRNA possesses many types of base modifications whose enzymatic regulations remain to be fully elucidated. It was reported that impaired tRNA nuclear-cytoplasmic export links DNA damage and cell-cycle checkpoint. Furthermore, a variety of additional functions of tRNA, beyond its translation of the genetic code, have emerged rapidly. For instance, tRNA cleavage is a conserved part of the responses to a variety of stresses in eukaryotic cells. Age-associated or tissue-specific tRNA fragmentation has also been observed. Several papers suggested that some of these tRNA fragments might be involve in the cellular RNA interference (RNAi) system. These exciting data, have lead to this call for a Research Topic, that plans to revisit and summarize the molecular biology of tRNA. Beyond the topics outlined above, we have highlighted recent developments in bioinformatics tools and databases for tRNA analyses.

Synthetic DNA and RNA Programming

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ISBN: 9783039217342 9783039217359 Year: Pages: 188 DOI: 10.3390/books978-3-03921-735-9 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:16
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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.

Keywords

fluorescent reporter --- live cell imaging --- microRNA quantification --- optogenetics --- small molecule drug screening --- Escherichia coli --- recombinant protein production --- gene overexpression --- growth effect --- ASKA collection --- codon bias --- branched-chain amino acids --- gene ontology --- genetic code expansion --- protein kinase B --- phosphoinositide dependent kinase 1 --- phosphoseryl-tRNA synthetase --- tRNASep --- alanyl-tRNA synthetase --- class II aminoacyl-tRNA synthetase --- expanded genetic code --- lysine acetylation --- posttranslational modification --- genetic code expansion --- transfer RNA --- synthetic biology --- non-canonical amino acids --- selenocysteine --- genetic code expansion --- release factor 1 --- amber stop codon suppression --- M. jannaschii orthogonal pair --- fluorescence-based screen --- cyclic peptides --- biopharmaceuticals --- mRNA display --- yeast two hybrid --- tRNASer --- mistranslation --- anticodon --- functional conservation --- alternative amino acid and nucleotide repertoires --- alternative core cellular chemistries --- biocontainment --- genetic firewall --- genetic isolation --- orthogonal central dogma of molecular biology --- synthetic life --- xenobiology --- genome engineering --- synthetic biology --- yeasts --- Metschnikowia --- genetic tools --- DNA delivery --- CUG-Ser --- reverse polymerization --- tRNA editing --- tRNA repair --- protein engineering --- synthetic biology --- tRNA --- misacylation --- indirect tRNA aminoacylation --- AspRS --- GluRS-like --- genetic code expansion --- genome synthesis --- genome editing --- microRNA --- protein modification --- RNA metabolism --- tRNA --- synthetic biology --- unnatural amino acids --- unnatural nucleotides

Thermophiles and Thermozymes

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ISBN: 9783038978169 9783038978176 Year: Pages: 198 DOI: 10.3390/books978-3-03897-817-6 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General)
Added to DOAB on : 2019-04-25 16:37:17
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Interest in the study of life in hot environments, both with respect to the inhabiting microorganisms and the enzymes they produce, is currently very high. The biological mechanisms responsible for the resistance to high temperatures are not yet fully understood, whereas thermostability is a highly required feature for industrial applications. In this e-book, the invited authors provide diverse evidence contributing to the understanding of such mechanisms and the unlocking of the biotechnological potential of thermophiles and thermozymes.

The Origin and Early Evolution of Life: Prebiotic Chemistry of Biomolecules

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ISBN: 9783039216062 9783039216079 Year: Pages: 288 DOI: 10.3390/books978-3-03921-607-9 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Chemistry (General)
Added to DOAB on : 2019-12-09 11:49:16
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Studying the origin of life is one of man’s greatest achievements over the last sixty years. The fields of interest encompassed by this quest are multiple and interdisciplinary: chemistry, physics, biology, biochemistry, mathematics, geology but also statistics, atmospheric science, meteorology, oceanography, and astrophysics. Recent scientific discoveries, such as water on Mars and the existence of super-Earths with atmospheres similar to primordial Earth, have pushed researchers to simulate prebiotic conditions in explaining the abiotic formation of molecules essential to life. This collection of articles offers an overview of recent discoveries in the field of prebiotic chemistry of biomolecules, their formation and selection, and the evolution of complex chemical systems.

Keywords

origin of life --- systems chemistry --- Chemomimesis --- Molecular Darwinism --- origin of life --- prebiotic chemistry --- thiol-rich peptides --- cysteine --- aminonitriles --- imidazoles --- origin of life --- prebiotic chemistry --- nucleotide and nucleoside synthesis --- protein design --- novel metalloproteins --- binary patterned amino acid sequences --- prebiotic chemistry --- population growth --- replication --- growth order --- Darwinian evolution --- selection --- origin of life --- abiogenesis --- carbon fixation --- hydrothermal vents --- electrochemistry --- reduction --- digit multiplicity --- information --- transmission --- encoding --- translation --- diversity --- function --- origin of life --- layered double hydroxide (LDH) clay --- pentose diphosphate --- pentopyranose nucleic acid --- arabinopyranose nucleic acid --- RNA --- base pairing --- purine precursor --- inosine --- AICAR --- peptide/RNA world --- prebiotic information system --- translation and the genetic code --- bridge peptide and aaRS --- ribozyme and tRNA --- tRNA and mRNA --- coevolution of translation machine and the genetic code --- MVC architecture pattern and biological information --- numerical codons --- AnyLogic software for computer simulation of translation machine --- phosphoryl transfer --- metabolism --- energy currency --- mixed anhydride --- origin of life --- hypercycle --- Monte Carlo --- prebiotic chemistry --- carbamic acid --- carbon dioxide-ammonia ices --- infrared spectra --- anharmonicity --- origin of life --- metabolism --- phosphates --- network expansion simulation --- thermodynamic bottleneck --- molecular clocks --- ab initio molecular dynamics --- catalysis --- prebiotic soup --- origins of life --- aldol reaction --- mechanochemistry --- minerals --- monosaccharides --- prebiotic chemistry --- prebiotic polymerization --- nucleotide oligomerization --- abasic oligomers --- nucleotide stability --- stability as a selection pressure --- dry-wet cycles --- genetic code origin --- tRNA accretion model --- tRNA-synthetase --- metabolism --- thioester --- nucleotidyltransferases --- early peptides --- ribosome --- n/a

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