Enzymic editing mechanisms and the origin of biological information transfer

1984 ◽  
Vol 107 (3) ◽  
pp. 387-403 ◽  
Author(s):  
Grant R. Lambert
Keyword(s):  
Information Transfer ◽  
Biological Information

scholarly journals Biodiversity of CS–proteoglycan sulphation motifs: chemical messenger recognition modules with roles in information transfer, control of cellular behaviour and tissue morphogenesis

2018 ◽  
Vol 475 (3) ◽  
pp. 587-620 ◽  
Author(s):  
Anthony Hayes ◽  
Kazuyuki Sugahara ◽  
Brooke Farrugia ◽  
John M. Whitelock ◽  
Bruce Caterson ◽  
...  
Keyword(s):  
Information Transfer ◽  
Enzyme Inhibitors ◽  
Chondroitin Sulphate ◽  
Chain Structure ◽  
Bioactive Molecules ◽  
Biological Information ◽  
Extracellular Milieu ◽  
Overwhelming Evidence ◽  
Chemical Messenger ◽  
Cellular Behaviour

Chondroitin sulphate (CS) glycosaminoglycan chains on cell and extracellular matrix proteoglycans (PGs) can no longer be regarded as merely hydrodynamic space fillers. Overwhelming evidence over recent years indicates that sulphation motif sequences within the CS chain structure are a source of significant biological information to cells and their surrounding environment. CS sulphation motifs have been shown to interact with a wide variety of bioactive molecules, e.g. cytokines, growth factors, chemokines, morphogenetic proteins, enzymes and enzyme inhibitors, as well as structural components within the extracellular milieu. They are therefore capable of modulating a panoply of signalling pathways, thus controlling diverse cellular behaviours including proliferation, differentiation, migration and matrix synthesis. Consequently, through these motifs, CS PGs play significant roles in the maintenance of tissue homeostasis, morphogenesis, development, growth and disease. Here, we review (i) the biodiversity of CS PGs and their sulphation motif sequences and (ii) the current understanding of the signalling roles they play in regulating cellular behaviour during tissue development, growth, disease and repair.

scholarly journals Vesicular Transport of Encapsulated microRNA between Glial and Neuronal Cells

2020 ◽  
Vol 21 (14) ◽  
pp. 5078 ◽  
Author(s):  
Walter J. Lukiw ◽  
Aileen I. Pogue
Keyword(s):  
Information Transfer ◽  
Biological Information ◽  
Messenger Rnas ◽  
Innate Immune Signaling ◽  
Cells Of Origin ◽  
Metabolic Products ◽  
Inflammatory Phenotype ◽  
The Central Nervous System ◽  
Neuro Inflammation ◽  
End Stage

Exosomes (EXs) and extracellular microvesicles (EMVs) represent a diverse assortment of plasma membrane-derived nanovesicles, 30–1000 nm in diameter, released by all cell lineages of the central nervous system (CNS). They are examples of a very active and dynamic form of extracellular communication and the conveyance of biological information transfer essential to maintain homeostatic neurological functions and contain complex molecular cargoes representative of the cytoplasm of their cells of origin. These molecular cargoes include various mixtures of proteins, lipids, proteolipids, cytokines, chemokines, carbohydrates, microRNAs (miRNA) and messenger RNAs (mRNA) and other components, including end-stage neurotoxic and pathogenic metabolic products, such as amyloid beta (Aβ) peptides. Brain microglia, for example, respond to both acute CNS injuries and degenerative diseases with complex reactions via the induction of a pro-inflammatory phenotype, and secrete EXs and EMVs enriched in selective pathogenic microRNAs (miRNAs) such as miRNA-34a, miRNA-125b, miRNA-146a, miRNA-155, and others that are known to promote neuro-inflammation, induce complement activation, disrupt innate–immune signaling and deregulate the expression of neuron-specific phosphoproteins involved in neurotropism and synaptic signaling. This communication will review our current understanding of the trafficking of miRNA-containing EXs and EMVs from astrocytes and “activated pro-inflammatory” microglia to target neurons in neurodegenerative diseases with an emphasis on Alzheimer’s disease wherever possible.

scholarly journals Insuperable problems of the genetic code initially emerging in an RNA World

2017 ◽  
Author(s):  
Peter R Wills ◽  
Charles W Carter
Keyword(s):  
Protein Synthesis ◽  
Information Processing ◽  
Natural Selection ◽  
Information Transfer ◽  
Rna World ◽  
Biological Information ◽  
Universal System ◽  
Biological Information Processing ◽  
Relationship Of ◽  
The Relationship

AbstractDifferential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide•RNA world.

scholarly journals Nuclear magnetic resonance studies of ribonucleic acids

2003 ◽  
Vol 17 (2-3) ◽  
pp. 537-547 ◽  
Author(s):  
Oliver Ohlenschläger ◽  
Jens Wöhnert ◽  
Ramadurai Ramachandran ◽  
Christian Sich ◽  
Matthias Görlach
Keyword(s):  
Information Transfer ◽  
Residual Dipolar Couplings ◽  
Protein Complexes ◽  
Pulse Sequences ◽  
Biological Information ◽  
Base Pairs ◽  
Stable Isotope Labelling ◽  
Ribonucleic Acids ◽  
Hydrogen Bonding Pattern ◽  
Essential Components

Ribonucleic acids (RNA) and RNA−protein complexes are essential components of biological information transfer, catalytic processes and are associated with regulatory functions. This broad range of biological functions is paralleled at the conformational level by a large number of non-canonical structural elements or sequences with non-standard backbone conformations, e.g., loops, bulges, pseudo-knots and complex tertiary folds. NMR spectroscopy has evolved to a powerful tool for the determination of ribonucleic acid structures of up to 20 kDa. Uniform or selective stable isotope labelling aids in solving assignment problems arising from the inherently limited chemical shift dispersion and overlap of resonances for larger nucleotide sequences. Recent developments of multi-dimensional heteronuclear NMR pulse sequences allow e.g., to directly observe the hydrogen bonding pattern of canonical Watson−Crick base pairs as well as of unusual types of base pairs, thereby opening up a fast access to secondary structure screening of RNA. Detailed conformational descriptions are obtained using conventional NOE andJcoupling-derived data, nowadays supplemented by information from residual dipolar couplings. The latter method also provides a new means for the probing of dynamical features of ribonucleic acids.

Genetic Information Transfer in Populations Under Selection

1997 ◽  
Vol 05 (01) ◽  
pp. 35-48
Author(s):  
N. Bartoloni
Keyword(s):  
Information Flow ◽  
Genetic Information ◽  
Information Transfer ◽  
Random Mating ◽  
Biological Information ◽  
Genetic Population ◽  
Information Measures ◽  
Selective Forces ◽  
Information Circulation

It is important to understand the dynamics of biological information in a genetic population for it determines the dynamics of energy and, thus, of matter. In another work we have initiated the characterization of a genetic population transmitting information from one generation to the next. In this work the genetic information flow under selection is analyzed in a genetic population under random mating. A one-locus diallelic model has been utilized in the derivations. Based upon the Schmalhausen's model of information circulation and the Shannon's theory of information we have focused on the analysis of information flow in the stage of transformation under the input of selective forces. The measures of information are important parameters to take account of when the process of populational evolution is analyzed. Several expressions relating information measures with selection coefficients corresponding to each genotype have been obtained. They are conditional entropies and mutual information (information transfer). Finally, a numerical survey employing a great deal of fitness values has been performed.

scholarly journals Mapping the dynamic transfer functions of epigenome editing

2021 ◽  
Author(s):  
Jessica B. Lee ◽  
Leandra M. Caywood ◽  
Jennifer Y. Lo ◽  
Nicholas Levering ◽  
Albert J. Keung
Keyword(s):  
Information Transfer ◽  
Transfer Functions ◽  
Stem Cell Differentiation ◽  
Biological Information ◽  
Fluorescent Reporter ◽  
Epigenome Editing ◽  
Eukaryotic Promoter ◽  
Physiological Processes ◽  
Signaling Components ◽  
Rich Content

AbstractBiological information can be encoded in the dynamics of signaling components which has been implicated in a broad range of physiological processes including stress response, oncogenesis, and stem cell differentiation. To study the complexity of information transfer across the eukaryotic promoter, we screened 119 dynamic conditions—modulating the frequency, intensity, and pulse width of light—regulating the binding of an epigenome editor to a fluorescent reporter. This system revealed highly tunable gene expression and filtering behaviors and provided the most comprehensive quantification to date of the maximum amount of information that can be reliably transferred across a promoter as ∼1.7 bits. Using a library of over 100 orthogonal epigenome editors, we further determined that chromatin state could be used to tune mutual information and expression levels, as well as completely alter the input-output transfer function of the promoter. This system unlocks the information-rich content of eukaryotic epigenome editing.

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