The sugar code: letters and vocabulary, writers, editors and readers and biosignificance of functional glycan–lectin pairing

2019 ◽  
Vol 476 (18) ◽  
pp. 2623-2655 ◽  
Author(s):  
Herbert Kaltner ◽  
José Abad-Rodríguez ◽  
Anthony P. Corfield ◽  
Jürgen Kopitz ◽  
Hans-Joachim Gabius
Keyword(s):  
Information Transfer ◽  
Structural Complexity ◽  
Structural Variations ◽  
Carbohydrate Recognition Domains ◽  
Random Assortment ◽  
Specific Receptors ◽  
Spatial Presentation ◽  
Biochemical Signals ◽  
Enzymatic Machinery ◽  
Lectin Recognition

Abstract Ubiquitous occurrence in Nature, abundant presence at strategically important places such as the cell surface and dynamic shifts in their profile by diverse molecular switches qualifies the glycans to serve as versatile biochemical signals. However, their exceptional structural complexity often prevents one noting how simple the rules of objective-driven assembly of glycan-encoded messages are. This review is intended to provide a tutorial for a broad readership. The principles of why carbohydrates meet all demands to be the coding section of an information transfer system, and this at unsurpassed high density, are explained. Despite appearing to be a random assortment of sugars and their substitutions, seemingly subtle structural variations in glycan chains by a sophisticated enzymatic machinery have emerged to account for their specific biological meaning. Acting as ‘readers’ of glycan-encoded information, carbohydrate-specific receptors (lectins) are a means to turn the glycans’ potential to serve as signals into a multitude of (patho)physiologically relevant responses. Once the far-reaching significance of this type of functional pairing has become clear, the various modes of spatial presentation of glycans and of carbohydrate recognition domains in lectins can be explored and rationalized. These discoveries are continuously revealing the intricacies of mutually adaptable routes to achieve essential selectivity and specificity. Equipped with these insights, readers will gain a fundamental understanding why carbohydrates form the third alphabet of life, joining the ranks of nucleotides and amino acids, and will also become aware of the importance of cellular communication via glycan–lectin recognition.

Information flow in the nervous system

1993 ◽  
Vol 1 (1) ◽  
pp. 31-39
Author(s):  
Arnold Burgen
Keyword(s):  
Information Flow ◽  
Information Transfer ◽  
Sensory Information ◽  
Nerve Fibres ◽  
Ionic Transfer ◽  
Electrical Pulses ◽  
Specific Receptors ◽  
Stored Information ◽  
High Level ◽  
Memory And Recall

Information is carried along nerve fibres by electrical pulses generated by ionic transfer; it is digitally coded. Information transfer between nerve cells depends on the release of a chemical transmitter which acts on specific receptors on the second neurone. This is a non-digital, analogue process which is highly non-linear. It involves the summation of inputs from highly divergent sources. In sensory systems such as vision, extensive compression, feature extraction and other high-level processing occur before presentation to the cerebral cortex, where a massive expansion in distribution of information occurs. Huge numbers of neurones are involved in the central presentation of even simple sensory information. This is because the neural events are relatively slow, so that a massive parallel information flow and processing occurs. Learning and memory involve changes in synaptic efficiency and the development of new stable connective patterns. Memory and recall must involve a comparison of contemporary events with stored information, but cannot involve a one-on-one comparison because it can deal with extensive transformation of sensory information.

scholarly journals Vegetation Structural Complexity and Biodiversity Across Elevation Gradients in the Great Smoky Mountains

2020 ◽  
Author(s):  
Jonathan Walter ◽  
Atticus Stovall ◽  
Jeff Atkins
Keyword(s):  
Forest Structure ◽  
Vegetation Structure ◽  
Vascular Plant ◽  
Structural Complexity ◽  
Plant Biodiversity ◽  
Structural Variations ◽  
Elevation Gradients ◽  
Great Smoky Mountains ◽  
Complexity Metrics ◽  
Smoky Mountains

Questions: Elevation, biodiversity, and forest structure are commonly correlated, but their relationships near the positive extremes of biodiversity and elevation are unclear. We asked 1) How does forest structure vary with elevation in a high biodiversity, high topographic complexity region? 2) Does forest structure predict vascular plant biodiversity? 3) Is plant biodiversity more strongly related to elevation or to forest structure? Location: Great Smoky Mountains National Park, USAMethods: We used terrestrial LiDAR scanning (TLS) to characterize vegetation structure in 12 forest plots. We combined two new canopy structural complexity metrics with traditional TLS-derived forest structural metrics and vascular plant biodiversity data to investigate correlations among forest structure metrics, biodiversity, and elevation. Results: Forest structure varied widely across plots spanning the elevational range of GRSM. Our new measures of canopy density (Depth) and structural complexity (σDepth) were sensitive to structural variations and effectively summarized horizontal and vertical dimensions of structural complexity. Vascular plant biodiversity was negatively correlated with elevation, and more strongly positively correlated with vegetation structure variables. Conclusions: The strong correlations we observed between canopy structural complexity and biodiversity suggest that structural complexity metrics could be used to assay plant biodiversity over large areas in concert with airborne and spaceborne platforms.

The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle

2021 ◽  
Vol 13 (1) ◽  
pp. 81-108 ◽  
Author(s):  
C. Arnosti ◽  
M. Wietz ◽  
T. Brinkhoff ◽  
J.-H. Hehemann ◽  
D. Probandt ◽  
...  
Keyword(s):  
Organic Matter ◽  
Phytoplankton Biomass ◽  
Current Knowledge ◽  
Large Fraction ◽  
Molecular Ecology ◽  
Structural Complexity ◽  
Future Research ◽  
Carbohydrate Chemistry ◽  
Enzymatic Machinery ◽  
Shed Light

Polysaccharides are major components of macroalgal and phytoplankton biomass and constitute a large fraction of the organic matter produced and degraded in the ocean. Until recently, however, our knowledge of marine polysaccharides was limited due to their great structural complexity, the correspondingly complicated enzymatic machinery used by microbial communities to degrade them, and a lack of readily applied means to isolate andcharacterize polysaccharides in detail. Advances in carbohydrate chemistry, bioinformatics, molecular ecology, and microbiology have led to new insights into the structures of polysaccharides, the means by which they are degraded by bacteria, and the ecology of polysaccharide production and decomposition. Here, we survey current knowledge, discuss recent advances, and present a new conceptual model linking polysaccharide structural complexity and abundance to microbially driven mechanisms of polysaccharide processing. We conclude by highlighting specific future research foci that will shed light on this central but poorly characterized component of the marine carbon cycle.

scholarly journals Lipoteichoic acid of Streptococcus oralis Uo5: a novel biochemical structure comprising an unusual phosphorylcholine substitution pattern compared to Streptococcus pneumoniae

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Nicolas Gisch ◽  
Dominik Schwudke ◽  
Simone Thomsen ◽  
Nathalie Heß ◽  
Regine Hakenbeck ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Teichoic Acid ◽  
Structural Complexity ◽  
Lipoteichoic Acid ◽  
Close Relative ◽  
Structural Variations ◽  
Wall Teichoic Acid ◽  
Substitution Pattern ◽  
Type Iv ◽  
Streptococcus Oralis

Abstract Members of the Mitis group of streptococci possess teichoic acids (TAs) as integral components of their cell wall that are unique among Gram-positive bacteria. Both, lipoteichoic (LTA) and wall teichoic acid, are formed by the same biosynthetic pathway, are of high complexity and contain phosphorylcholine (P-Cho) residues. These residues serve as anchors for choline-binding proteins (CBPs), some of which have been identified as virulence factors of the human pathogen Streptococcus pneumoniae. We investigated the LTA structure of its close relative Streptococcus oralis. Our analysis revealed that S. oralis Uo5 LTA has an overall architecture similar to pneumococcal LTA (pnLTA) and can be considered as a subtype of type IV LTA. Its structural complexity is even higher than that of pnLTA and its composition differs in number and type of carbohydrate moieties, inter-residue connectivities and especially the P-Cho substitution pattern. Here, we report the occurrence of a saccharide moiety substituted with two P-Cho residues, which is unique as yet in bacterial derived surface carbohydrates. Finally, we could link the observed important structural variations between S. oralis and S. pneumoniae LTA to the divergent enzymatic repertoire for their TA biosynthesis.

Structural and biochemical basis of a marine bacterial glycoside hydrolase family 2 β-glycosidase with broad substrate specificity

2021 ◽  
Author(s):  
Jian Yang ◽  
Shubo Li ◽  
Yu Liu ◽  
Ru Li ◽  
Lijuan Long
Keyword(s):  
Substrate Specificity ◽  
Glycoside Hydrolase ◽  
Structural Complexity ◽  
Glycoside Hydrolase Family ◽  
Biochemical Basis ◽  
Broad Substrate Specificity ◽  
Biochemical Analyses ◽  
Transformation Of Organic Matter ◽  
Enzymatic Machinery ◽  
Hydrolase Family

Uronic acids are commonly found in marine polysaccharides and increase structural complexity sanand intrinsic recalcitrance to enzymatic attack. The glycoside hydrolase family 2 (GH2) include proteins that target sugar conjugates with hexuronates and are involved in the catabolism and cycling of marine polysaccharides. Here, we reported a novel GH2, Aq GalA from a marine algae-associated Bacteroidetes with broad-substrate specificity. Biochemical analyses revealed that Aq GalA exhibits hydrolyzing activities against β-galacturonide, β-glucuronide, and β-galactopyranoside via retaining mechanisms. We solved the Aq GalA crystal structure in complex with galacturonic acid (GalA) and showed (via mutagenesis) that charge characteristics at uronate-binding subsites controlled substrate selectivity for uronide hydrolysis. Additionally, conformational flexibility of the Aq GalA active site pocket was proposed as a key component for broad substrate enzyme selectivity. Our Aq GalA structural and functional data augments the current understanding of substrate recognition of GH2 enzymes and provided key insights into the bacterial use of uronic acid containing polysaccharides. IMPORTANCE The decomposition of algal glycans driven by marine bacterial communities represents one of the largest heterotrophic transformation of organic matter fueling marine food webs and global carbon cycling. However, our knowledge of the carbohydrate cycling is limited due to structural complexity of marine polysaccharides and the complicated enzymatic machinery of marine microbes. To degrade algal glycan, marine bacteria such as members of Bacteroidetes produce a complex repertoire of carbohydrate-active enzymes (CAZymes) matching the structural specificity of the different carbohydrates. In this study, we investigated an extracellular GH2 β-glycosidase, Aq GalA from a marine Bacteroidetes to identify the key components responsible for glycuronides recognition and hydrolysis. The broad substrate specificity of Aq GalA against glycosides with diverse stereochemical substitutions indicates its potential in processing complex marine polysaccharides. Our findings promote a better understanding of microbially-driven mechanisms of marine carbohydrate cycling.

Glycobiomarkers by glycoproteomics and glycan profiling (glycomics): emergence of functionality

2011 ◽  
Vol 39 (1) ◽  
pp. 399-405 ◽  
Author(s):  
Hans-Joachim Gabius
Keyword(s):  
Growth Regulation ◽  
Structural Complexity ◽  
Cancer Growth ◽  
Glycan Structure ◽  
Promising Candidate ◽  
Functional Consequences ◽  
Glycan Profiling ◽  
Specific Receptors ◽  
Analytical Processing ◽  
New Biomarkers

Glycans stand out from all classes of biomolecules because of their unsurpassed structural complexity. This is generated by variability in anomeric status of the glycosidic bond and its linkage points, ring size, potential for branching and introduction of diverse site-specific substitutions. What poses an enormous challenge for analytical processing is, at the same time, the basis for the fingerprint-like glycomic profiles of glycoconjugates and cells. What's more, the glycosylation machinery is sensitive to disease manifestations, earning glycan assembly a reputation as a promising candidate to identify new biomarkers. Backing this claim for a perspective in clinical practice are recent discoveries that even seemingly subtle changes in the glycan structure of glycoproteins, such as a N-glycan core substitution by a single sugar moiety, have far-reaching functional consequences. They are brought about by altering the interplay between the glycan and (i) its carrier protein and (ii) specific receptors (lectins). Glycan attachment thus endows the protein with a molecular switch and new recognition sites. Co-ordinated regulation of glycan display and presentation of the cognate lectin, e.g. in cancer growth regulation exerted by a tumour suppressor, further exemplifies the broad functional dimension inherent to the non-random shifts in glycosylation. Thus studies on glycobiomarkers converge with research on how distinct carbohydrate determinants are turned into bioactive signals.

Crystalloid Inclusions in Hepatocyte Mitochondria and Their Similarity to Cytoplasmic Crystalloids

1974 ◽  
Vol 32 ◽  
pp. 198-199
Author(s):  
Odell T. Minick ◽  
Hidejiro Yokoo
Keyword(s):  
Liver Disease ◽  
Alcoholic Liver Disease ◽  
Special Interest ◽  
Structural Variations ◽  
Mitochondrial Alterations ◽  
The Matrix ◽  
Crystalloid Inclusions ◽  
Liver Biopsies

Mitochondrial alterations were studied in 25 liver biopsies from patients with alcoholic liver disease. Of special interest were the morphologic resemblance of certain fine structural variations in mitochondria and crystalloid inclusions. Four types of alterations within mitochondria were found that seemed to relate to cytoplasmic crystalloids.Type 1 alteration consisted of localized groups of cristae, usually oriented in the long direction of the organelle (Fig. 1A). In this plane they appeared serrated at the periphery with blind endings in the matrix. Other sections revealed a system of equally-spaced diagonal lines lengthwise in the mitochondrion with cristae protruding from both ends (Fig. 1B). Profiles of this inclusion were not unlike tangential cuts of a crystalloid structure frequently seen in enlarged mitochondria described below.

Infection of Escherichia coli with bacteriophages

1969 ◽  
Vol 27 ◽  
pp. 370-371
Author(s):  
Manfred E. Bayer
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Cell Surface ◽  
Virus Type ◽  
Infection Process ◽  
Adsorption Site ◽  
The Other ◽  
Specific Receptors ◽  
Bacterial Receptors

The first step in the infection of a bacterium by a virus consists of a collision between cell and bacteriophage. The presence of virus-specific receptors on the cell surface will trigger a number of events leading eventually to release of the phage nucleic acid. The execution of the various "steps" in the infection process varies from one virus-type to the other, depending on the anatomy of the virus. Small viruses like ØX 174 and MS2 adsorb directly with their capsid to the bacterial receptors, while other phages possess attachment organelles of varying complexity. In bacteriophages T3 (Fig. 1) and T7 the small conical processes of their heads point toward the adsorption site; a welldefined baseplate is attached to the head of P22; heads without baseplates are not infective.

Conformation of eukaryotic ribosomal RNAs

1983 ◽  
Vol 41 ◽  
pp. 592-593
Author(s):  
M. Boublik ◽  
G. Thornton ◽  
G. Oostergetel ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Molecular Weight ◽  
Mass Measurement ◽  
Carbon Film ◽  
Structural Complexity ◽  
Scanning Transmission Electron Microscope ◽  
Electron Microscopic ◽  
Pure Nitrogen ◽  
Freeze Dried ◽  
Scanning Transmission ◽  
Partially Unfolded

Understanding the structural complexity of ribosomes and their role in protein synthesis requires knowledge of the conformation of their components - rRNAs and proteins. Application of dedicated scanning transmission electron microscope (STEM), electrical discharge of the support carbon film in an atmosphere of pure nitrogen, and determination of the molecular weight of individual rRNAs enabled us to obtain high resolution electron microscopic images of unstained freeze-dried rRNA molecules from BHK cells in a form suitable for evaluation of their 3-D structure. Preliminary values for the molecular weight of 28S RNA from the large and 18S RNA from the small ribosomal subunits as obtained by mass measurement were 1.84 x 106 and 0.97 x 106, respectively. Conformation of rRNAs consists, in general, of alternating segments of intramolecular hairpin stems and single stranded loops in a proportion which depends on their ionic environment, the Mg++ concentration in particular. Molecules of 28S RNA (Fig. 1) and 18S RNA (not shown) obtained by freeze-drying from a solution of 60 mM NH+4 acetate and 2 mM Mg++ acetate, pH 7, appear as partially unfolded coils with compact cores suggesting a high degree of ordered secondary structure.

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