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https://www.readbyqxmd.com/read/28441334/peptidyl-transferase-center-and-the-emergence-of-the-translation-system
#1
Savio Torres de Farias, Thais Gaudêncio Rêgo, Marco V José
In this work, the three-dimensional (3D) structure of the ancestral Peptidyl Transferase Center (PTC) built by concatamers of ancestral sequences of tRNAs was reconstructed, and its possible interactions with tRNAs molecules were analyzed. The 3D structure of the ancestral PTC was also compared with the current PTC of T. thermophilus. Docking experiments between the ancestral PTC and tRNAs suggest that in the origin of the translation system, the PTC functioned as an adhesion center for tRNA molecules. The approximation of tRNAs charged with amino acids to the PTC permitted peptide synthesis without the need of a genetic code...
April 25, 2017: Life
https://www.readbyqxmd.com/read/28420220/the-maximal-c%C3%A2-self-complementary-trinucleotide-circular-code-x-in-genes-of-bacteria-archaea-eukaryotes-plasmids-and-viruses
#2
Christian J Michel
In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses...
April 18, 2017: Life
https://www.readbyqxmd.com/read/28397774/small-and-random-peptides-an-unexplored-reservoir-of-potentially-functional-primitive-organocatalysts-the-case-of-seryl-histidine
#3
REVIEW
Rafal Wieczorek, Katarzyna Adamala, Tecla Gasperi, Fabio Polticelli, Pasquale Stano
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth...
April 9, 2017: Life
https://www.readbyqxmd.com/read/28383509/self-referential-encoding-on-modules-of-anticodon-pairs-roots-of-the-biological-flow-system
#4
REVIEW
Romeu Cardoso Guimarães
The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes-structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process-anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle...
April 6, 2017: Life
https://www.readbyqxmd.com/read/28383497/evo-seti-a-mathematical-tool-for-cladistics-evolution-and-seti
#5
Claudio Maccone
The discovery of new exoplanets makes us wonder where each new exoplanet stands along its way to develop life as we know it on Earth. Our Evo-SETI Theory is a mathematical way to face this problem. We describe cladistics and evolution by virtue of a few statistical equations based on lognormal probability density functions (pdf) in the time. We call b-lognormal a lognormal pdf starting at instant b (birth). Then, the lifetime of any living being becomes a suitable b-lognormal in the time. Next, our "Peak-Locus Theorem" translates cladistics: each species created by evolution is a b-lognormal whose peak lies on the exponentially growing number of living species...
April 6, 2017: Life
https://www.readbyqxmd.com/read/28383486/prebiotic-factors-influencing-the-activity-of-a-ligase-ribozyme
#6
Fabrizio Anella, Christophe Danelon
An RNA-lipid origin of life scenario provides a plausible route for compartmentalized replication of an informational polymer and subsequent division of the container. However, a full narrative to form such RNA protocells implies that catalytic RNA molecules, called ribozymes, can operate in the presence of self-assembled vesicles composed of prebiotically relevant constituents, such as fatty acids. Hereby, we subjected a newly engineered truncated variant of the L1 ligase ribozyme, named tL1, to various environmental conditions that may have prevailed on the early Earth with the objective to find a set of control parameters enabling both tL1-catalyzed ligation and formation of stable myristoleic acid (MA) vesicles...
April 6, 2017: Life
https://www.readbyqxmd.com/read/28379164/what-froze-the-genetic-code
#7
Lluís Ribas de Pouplana, Adrian Gabriel Torres, Àlbert Rafels-Ybern
The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true...
April 5, 2017: Life
https://www.readbyqxmd.com/read/28346388/thermal-condensation-of-glycine-and-alanine-on-metal-ferrite-surface-primitive-peptide-bond-formation-scenario
#8
Md Asif Iqubal, Rachana Sharma, Sohan Jheeta, Kamaluddin
The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe₂O₄), cobalt ferrite (CoFe₂O₄), copper ferrite (CuFe₂O₄), zinc ferrite (ZnFe₂O₄), and manganese ferrite (MnFe₂O₄) nanoparticles surfaces, in the temperature range from 50-120 °C for 1-35 days, without applying any wetting/drying cycles...
March 27, 2017: Life
https://www.readbyqxmd.com/read/28333103/the-genetic-code-and-rna-amino-acid-affinities
#9
REVIEW
Michael Yarus
A significant part of the genetic code likely originated via a chemical interaction, which should be experimentally verifiable. One possible verification relates bound amino acids (or perhaps their activated congeners) and ribonucleotide sequences within cognate RNA binding sites. To introduce this interaction, I first summarize how amino acids function as targets for RNA binding. Then the experimental method for selecting relevant RNA binding sites is characterized. The selection method's characteristics are related to the investigation of the RNA binding site model treated at the outset...
March 23, 2017: Life
https://www.readbyqxmd.com/read/28335420/efforts-and-challenges-in-engineering-the-genetic-code
#10
REVIEW
Xiao Lin, Allen Chi Shing Yu, Ting Fung Chan
This year marks the 48th anniversary of Francis Crick's seminal work on the origin of the genetic code, in which he first proposed the "frozen accident" hypothesis to describe evolutionary selection against changes to the genetic code that cause devastating global proteome modification. However, numerous efforts have demonstrated the viability of both natural and artificial genetic code variations. Recent advances in genetic engineering allow the creation of synthetic organisms that incorporate noncanonical, or even unnatural, amino acids into the proteome...
March 14, 2017: Life
https://www.readbyqxmd.com/read/28272354/micrometer-scale-membrane-transition-of-supported-lipid-bilayer-membrane-reconstituted-with-cytosol-of-dictyostelium-discoideum
#11
Kei Takahashi, Taro Toyota
The transformation of the supported lipid bilayer (SLB) membrane by extracted cytosol from living resources, has recently drawn much attention. It enables us to address the question of whether the purified phospholipid SLB membrane, including lipids related to amoeba locomotion, which was discussed in many previous studies, exhibits membrane deformation in the presence of cytosol extracted from amoeba; Methods: In this report, a method for reconstituting a supported lipid bilayer (SLB) membrane, composed of purified phospholipids and cytosol extracted from Dictyostelium discoideum, is described...
March 7, 2017: Life
https://www.readbyqxmd.com/read/28264473/future-of-the-genetic-code
#12
REVIEW
Hong Xue, J Tze-Fei Wong
The methods for establishing synthetic lifeforms with rewritten genetic codes comprising non-canonical amino acids (NCAA) in addition to canonical amino acids (CAA) include proteome-wide replacement of CAA, insertion through suppression of nonsense codon, and insertion via the pyrrolysine and selenocysteine pathways. Proteome-wide reassignments of nonsense codons and sense codons are also under development. These methods enable the application of NCAAs to enrich both fundamental and applied aspects of protein chemistry and biology...
February 28, 2017: Life
https://www.readbyqxmd.com/read/28264444/highly-conserved-elements-and-chromosome-structure-evolution-in-mitochondrial-genomes-in-ciliates
#13
Roman A Gershgorin, Konstantin Yu Gorbunov, Oleg A Zverkov, Lev I Rubanov, Alexandr V Seliverstov, Vassily A Lyubetsky
Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models...
February 27, 2017: Life
https://www.readbyqxmd.com/read/28230768/bioinformatic-analysis-reveals-archaeal-trna-tyr-and-trna-trp-identities-in-bacteria
#14
Takahito Mukai, Noah M Reynolds, Ana Crnković, Dieter Söll
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins...
February 21, 2017: Life
https://www.readbyqxmd.com/read/28208827/on-the-uniqueness-of-the-standard-genetic-code
#15
Gabriel S Zamudio, Marco V José
In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and the non-degeneracy of the assignments of aminoacyl-tRNA synthetases (aaRSs) to amino acids; the wobbling property; the consideration that glycine was the first amino acid; the topological and symmetrical properties of both codes...
February 13, 2017: Life
https://www.readbyqxmd.com/read/28208756/homocysteine-editing-thioester-chemistry-coenzyme-a-and-the-origin-of-coded-peptide-synthesis-%C3%A2
#16
REVIEW
Hieronim Jakubowski
Aminoacyl-tRNA synthetases (AARSs) have evolved "quality control" mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols...
February 9, 2017: Life
https://www.readbyqxmd.com/read/28106741/the-role-of-lipid-membranes-in-life-s-origin
#17
REVIEW
David Deamer
At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups...
January 17, 2017: Life
https://www.readbyqxmd.com/read/28067845/selection-of-prebiotic-molecules-in-amphiphilic-environments
#18
Christian Mayer, Ulrich Schreiber, María J Dávila
A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution...
January 7, 2017: Life
https://www.readbyqxmd.com/read/28054992/mobility-of-a-mononucleotide-within-a-lipid-matrix-a-neutron-scattering-study
#19
Loreto Misuraca, Francesca Natali, Laura da Silva, Judith Peters, Bruno Demé, Jacques Ollivier, Tilo Seydel, Valerie Laux-Lesourd, Michael Haertlein, Giuseppe Zaccai, David Deamer, Marie Christine Maurel
An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction allowing the formation of RNA-like polymers, followed by encapsulation in lipid membranes. Here, we used neutron scattering and deuterium labelling to investigate 5'-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix...
January 4, 2017: Life
https://www.readbyqxmd.com/read/28035953/arsenite-as-an-electron-donor-for-anoxygenic-photosynthesis-description-of-three-strains-of-ectothiorhodospira-from-mono-lake-california-and-big-soda-lake-nevada
#20
Shelley Hoeft McCann, Alison Boren, Jaime Hernandez-Maldonado, Brendon Stoneburner, Chad W Saltikov, John F Stolz, Ronald S Oremland
Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes...
December 26, 2016: Life
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