Journal articles: 'Glycan code'

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Jones, Christopher J., and Cynthia K. Larive. "Cracking the glycan sequence code." Nature Chemical Biology 7, no. 11 (October 18, 2011): 758–59. http://dx.doi.org/10.1038/nchembio.696.

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Kaltner, Herbert, José Abad-Rodríguez, Anthony P. Corfield, Jürgen Kopitz, and Hans-Joachim Gabius. "The sugar code: letters and vocabulary, writers, editors and readers and biosignificance of functional glycan–lectin pairing." Biochemical Journal 476, no. 18 (September 24, 2019): 2623–55. http://dx.doi.org/10.1042/bcj20170853.

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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.

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Klein, Joshua, Luis Carvalho, and Joseph Zaia. "Application of network smoothing to glycan LC-MS profiling." Bioinformatics 34, no. 20 (May 22, 2018): 3511–18. http://dx.doi.org/10.1093/bioinformatics/bty397.

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Abstract Motivation Glycosylation is one of the most heterogeneous and complex protein post-translational modifications. Liquid chromatography coupled mass spectrometry (LC-MS) is a common high throughput method for analyzing complex biological samples. Accurate study of glycans require high resolution mass spectrometry. Mass spectrometry data contains intricate sub-structures that encode mass and abundance, requiring several transformations before it can be used to identify biological molecules, requiring automated tools to analyze samples in a high throughput setting. Existing tools for interpreting the resulting data do not take into account related glycans when evaluating individual observations, limiting their sensitivity. Results We developed an algorithm for assigning glycan compositions from LC-MS data by exploring biosynthetic network relationships among glycans. Our algorithm optimizes a set of likelihood scoring functions based on glycan chemical properties but uses network Laplacian regularization and optionally prior information about expected glycan families to smooth the likelihood and thus achieve a consistent and more representative solution. Our method was able to identify as many, or more glycan compositions compared to previous approaches, and demonstrated greater sensitivity with regularization. Our network definition was tailored to N-glycans but the method may be applied to glycomics data from other glycan families like O-glycans or heparan sulfate where the relationships between compositions can be expressed as a graph. Availability and implementation Built Executable http://www.bumc.bu.edu/msr/glycresoft/ and Source Code: https://github.com/BostonUniversityCBMS/glycresoft. Supplementary information Supplementary data are available at Bioinformatics online.

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Kellman, Benjamin P., Yujie Zhang, Emma Logomasini, Eric Meinhardt, Karla P. Godinez-Macias, Austin W. T. Chiang, James T. Sorrentino, et al. "A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)." Beilstein Journal of Organic Chemistry 16 (October 27, 2020): 2645–62. http://dx.doi.org/10.3762/bjoc.16.215.

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Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a clear glycan representation accessible to both computers and humans. Linear Code, a linearized and readily parsable glycan structure representation, is such a language. For this reason, Linear Code was adapted to represent reaction rules, but the syntax has drifted from its original description to accommodate new and originally unforeseen challenges. Here, we delineate the consensuses and inconsistencies that have arisen through this adaptation. We recommend options for a consensus-based extension of Linear Code that can be used for reaction rule specification going forward. Through this extension and specification of Linear Code to reaction rules, we aim to minimize inconsistent symbology thereby making glycan database queries easier. With a clear guide for generating reaction rule descriptions, glycan synthesis models will be more interoperable and reproducible thereby moving glycoinformatics closer to compliance with FAIR standards. Here, we present Linear Code for Reaction Rules (LiCoRR), version 1.0, an unambiguous representation for describing glycosylation reactions in both literature and code.

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Gabius, Hans-Joachim. "Glycans: bioactive signals decoded by lectins." Biochemical Society Transactions 36, no. 6 (November 19, 2008): 1491–96. http://dx.doi.org/10.1042/bst0361491.

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The glycan part of cellular glycoconjugates affords a versatile means to build biochemical signals. These oligosaccharides have an exceptional talent in this respect. They surpass any other class of biomolecule in coding capacity within an oligomer (code word). Four structural factors account for this property: the potential for variability of linkage points, anomeric position and ring size as well as the aptitude for branching (first and second dimensions of the sugar code). Specific intermolecular recognition is favoured by abundant potential for hydrogen/co-ordination bonds and for C–H/π-interactions. Fittingly, an array of protein folds has developed in evolution with the ability to select certain glycans from the natural diversity. The thermodynamics of this reaction profits from the occurrence of these ligands in only a few energetically favoured conformers, comparing favourably with highly flexible peptides (third dimension of the sugar code). Sequence, shape and local aspects of glycan presentation (e.g. multivalency) are key factors to regulate the avidity of lectin binding. At the level of cells, distinct glycan determinants, a result of enzymatic synthesis and dynamic remodelling, are being defined as biomarkers. Their presence gains a functional perspective by co-regulation of the cognate lectin as effector, for example in growth regulation. The way to tie sugar signal and lectin together is illustrated herein for two tumour model systems. In this sense, orchestration of glycan and lectin expression is an efficient means, with far-reaching relevance, to exploit the coding potential of oligosaccharides physiologically and medically.

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Alocci, Davide, Pavla Suchánková, Renaud Costa, Nicolas Hory, Julien Mariethoz, Radka Vařeková, Philip Toukach, and Frédérique Lisacek. "SugarSketcher: Quick and Intuitive Online Glycan Drawing." Molecules 23, no. 12 (December 5, 2018): 3206. http://dx.doi.org/10.3390/molecules23123206.

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SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e.g., GlycoCT) or quality images (e.g., svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The “quick mode” allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The “normal mode” integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.

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Dumych, Tetiana, Clarisse Bridot, Sébastien Gouin, Marc Lensink, Solomiya Paryzhak, Sabine Szunerits, Ralf Blossey, Rostyslav Bilyy, Julie Bouckaert, and Eva-Maria Krammer. "A Novel Integrated Way for Deciphering the Glycan Code for the FimH Lectin." Molecules 23, no. 11 (October 28, 2018): 2794. http://dx.doi.org/10.3390/molecules23112794.

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The fimbrial lectin FimH from uro- and enteropathogenic Escherichia coli binds with nanomolar affinity to oligomannose glycans exposing Manα1,3Man dimannosides at their non-reducing end, but only with micromolar affinities to Manα1,2Man dimannosides. These two dimannoses play a significantly distinct role in infection by E. coli. Manα1,2Man has been described early on as shielding the (Manα1,3Man) glycan that is more relevant to strong bacterial adhesion and invasion. We quantified the binding of the two dimannoses (Manα1,2Man and Manα1,3Man to FimH using ELLSA and isothermal microcalorimetry and calculated probabilities of binding modes using molecular dynamics simulations. Our experimentally and computationally determined binding energies confirm a higher affinity of FimH towards the dimannose Manα1,3Man. Manα1,2Man displays a much lower binding enthalpy combined with a high entropic gain. Most remarkably, our molecular dynamics simulations indicate that Manα1,2Man cannot easily take its major conformer from water into the FimH binding site and that FimH is interacting with two very different conformers of Manα1,2Man that occupy 42% and 28% respectively of conformational space. The finding that Manα1,2Man binding to FimH is unstable agrees with the earlier suggestion that E. coli may use the Manα1,2Man epitope for transient tethering along cell surfaces in order to enhance dispersion of the infection.

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Lopes, Nuno, Viviana G. Correia, Angelina S. Palma, and Catarina Brito. "Cracking the Breast Cancer Glyco-Code through Glycan-Lectin Interactions: Targeting Immunosuppressive Macrophages." International Journal of Molecular Sciences 22, no. 4 (February 17, 2021): 1972. http://dx.doi.org/10.3390/ijms22041972.

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The immune microenvironment of breast cancer (BC) is composed by high macrophage infiltrates, correlated with the most aggressive subtypes. Tumour-associated macrophages (TAM) within the BC microenvironment are key regulators of immune suppression and BC progression. Nevertheless, several key questions regarding TAM polarisation by BC are still not fully understood. Recently, the modulation of the immune microenvironment has been described via the recognition of abnormal glycosylation patterns at BC cell surface. These patterns rise as a resource to identify potential targets on TAM in the BC context, leading to the development of novel immunotherapies. Herein, we will summarize recent studies describing advances in identifying altered glycan structures in BC cells. We will focus on BC-specific glycosylation patterns known to modulate the phenotype and function of macrophages recruited to the tumour site, such as structures with sialylated or N-acetylgalactosamine epitopes. Moreover, the lectins present at the surface of macrophages reported to bind to such antigens, inducing tumour-prone TAM phenotypes, will also be highlighted. Finally, we will discuss and give our view on the potential and current challenges of targeting these glycan-lectin interactions to reshape the immunosuppressive landscape of BC.

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Kaltner, Herbert, and Hans-Joachim Gabius. "Sensing Glycans as Biochemical Messages by Tissue Lectins: The Sugar Code at Work in Vascular Biology." Thrombosis and Haemostasis 119, no. 04 (January 8, 2019): 517–33. http://dx.doi.org/10.1055/s-0038-1676968.

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AbstractAlthough a plethora of players has already been revealed to be engaged in the haemostatic system, a fundamental consideration of the molecular nature of information coding can give further explorations of the mechanisms of blood clotting, platelet functionality and vascular trafficking direction. By any measures, looking at ranges of occurrence and of potential for structural versatility, at strategic positioning to influence protein and cell sociology as well as at dynamics of processing and restructuring for phenotypic variability, using sugars as an alphabet of life for generating the glycan part of glycoconjugates is a success story. The handiwork by the complex system for glycan biosynthesis renders biochemical messages of exceptionally high coding capacity available. They are read and translated into cellular effects by receptors termed lectins. The different levels of regulation on both sides, that is, glycan and lectin, establish an intriguingly fine-tuned capacity for functional pairing. The emerging insights into the highly branched routes of glycosylation, into lectin structures up to complete characterization in solution and the shape of lectin networks, first obtained for the three selectins, now extended to considering many other C-type lectins, galectins and siglecs, as well as into intra- and inter-family cross-talk and cooperations are sure to push boundaries in our understanding of the molecular basis of haemostasis.

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Yusufi, Faraaz Noor Khan, Wonjun Park, May May Lee, and Dong-Yup Lee. "An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins." Bioprocess and Biosystems Engineering 32, no. 1 (May 6, 2008): 97–107. http://dx.doi.org/10.1007/s00449-008-0226-4.

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Mrázek, Hynek, Lenka Weignerová, Pavla Bojarová, Petr Novák, Ondřej Vaněk, and Karel Bezouška. "Carbohydrate synthesis and biosynthesis technologies for cracking of the glycan code: Recent advances." Biotechnology Advances 31, no. 1 (January 2013): 17–37. http://dx.doi.org/10.1016/j.biotechadv.2012.03.008.

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Xie, Wei, Kazue Kanehara, Ayaz Sayeed, and Davis T. W. Ng. "Intrinsic Conformational Determinants Signal Protein Misfolding to the Hrd1/Htm1 Endoplasmic Reticulum–associated Degradation System." Molecular Biology of the Cell 20, no. 14 (July 15, 2009): 3317–29. http://dx.doi.org/10.1091/mbc.e09-03-0231.

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Endoplasmic reticulum (ER) quality control mechanisms monitor the folding of nascent polypeptides of the secretory pathway. These are dynamic processes that retain folding proteins, promote the transport of conformationally mature proteins, and target misfolded proteins to ER-associated degradation (ERAD) pathways. Aided by the identification of numerous ERAD factors, late functions that include substrate extraction, ubiquitination, and degradation are fairly well described. By contrast, the mechanisms of substrate recognition remain mysterious. For some substrates, a specific N-linked glycan forms part of the recognition code but how it is read is incompletely understood. In this study, systematic analysis of model substrates revealed such glycans mark structural determinants that are sensitive to the overall folding state of the molecule. This strategy effectively generates intrinsic folding sensors that communicate with high fidelity to ERAD. Normally, these segments fold into the mature structure to pass the ERAD checkpoint. However, should a molecule fail to fold completely, they form a bipartite signal that comprises the unfolded local structure and adjacent enzymatically remodeled glycan. Only if both elements are present will the substrate be targeted to the ERAD pathway for degradation.

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Vogt, Marian Samuel, Gesa Felicitas Schmitz, Daniel Varón Silva, Hans-Ulrich Mösch, and Lars-Oliver Essen. "Structural base for the transfer of GPI-anchored glycoproteins into fungal cell walls." Proceedings of the National Academy of Sciences 117, no. 36 (August 24, 2020): 22061–67. http://dx.doi.org/10.1073/pnas.2010661117.

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The correct distribution and trafficking of proteins are essential for all organisms. Eukaryotes evolved a sophisticated trafficking system which allows proteins to reach their destination within highly compartmentalized cells. One eukaryotic hallmark is the attachment of a glycosylphosphatidylinositol (GPI) anchor to C-terminal ω-peptides, which are used as a zip code to guide a subset of membrane-anchored proteins through the secretory pathway to the plasma membrane. In fungi, the final destination of many GPI-anchored proteins is their outermost compartment, the cell wall. Enzymes of the Dfg5 subfamily catalyze the essential transfer of GPI-anchored substrates from the plasma membrane to the cell wall and discriminate between plasma membrane-resident GPI-anchored proteins and those transferred to the cell wall (GPI-CWP). We solved the structure of Dfg5 from a filamentous fungus and used in crystallo glycan fragment screening to reassemble the GPI-core glycan in a U-shaped conformation within its binding pocket. The resulting model of the membrane-bound Dfg5•GPI-CWP complex is validated by molecular dynamics (MD) simulations and in vivo mutants in yeast. The latter show that impaired transfer of GPI-CWPs causes distorted cell-wall integrity as indicated by increased chitin levels. The structure of a Dfg5•β1,3-glycoside complex predicts transfer of GPI-CWP toward the nonreducing ends of acceptor glycans in the cell wall. In addition to our molecular model for Dfg5-mediated transglycosylation, we provide a rationale for how GPI-CWPs are specifically sorted toward the cell wall by using GPI-core glycan modifications.

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Suhre, Karsten, Irena Trbojević-Akmačić, Ivo Ugrina, Dennis Mook-Kanamori, Tim Spector, Johannes Graumann, Gordan Lauc, and Mario Falchi. "Fine-Mapping of the Human Blood Plasma N-Glycome onto Its Proteome." Metabolites 9, no. 7 (June 26, 2019): 122. http://dx.doi.org/10.3390/metabo9070122.

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Most human proteins are glycosylated. Attachment of complex oligosaccharides to the polypeptide part of these proteins is an integral part of their structure and function and plays a central role in many complex disorders. One approach towards deciphering this human glycan code is to study natural variation in experimentally well characterized samples and cohorts. High-throughput capable large-scale methods that allow for the comprehensive determination of blood circulating proteins and their glycans have been recently developed, but so far, no study has investigated the link between both traits. Here we map for the first time the blood plasma proteome to its matching N-glycome by correlating the levels of 1116 blood circulating proteins with 113 N-glycan traits, determined in 344 samples from individuals of Arab, South-Asian, and Filipino descent, and then replicate our findings in 46 subjects of European ancestry. We report protein-specific N-glycosylation patterns, including a correlation of core fucosylated structures with immunoglobulin G (IgG) levels, and of trisialylated, trigalactosylated, and triantennary structures with heparin cofactor 2 (SERPIND2). Our study reveals a detailed picture of protein N-glycosylation and suggests new avenues for the investigation of its role and function in the associated complex disorders.

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Tsuchiya, Shinichiro, Issaku Yamada, and Kiyoko F. Aoki-Kinoshita. "GlycanFormatConverter: a conversion tool for translating the complexities of glycans." Bioinformatics 35, no. 14 (December 7, 2018): 2434–40. http://dx.doi.org/10.1093/bioinformatics/bty990.

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Abstract Motivation Glycans are biomolecules that take an important role in the biological processes of living organisms. They form diverse, complicated structures such as branched and cyclic forms. Web3 Unique Representation of Carbohydrate Structures (WURCS) was proposed as a new linear notation for uniquely representing glycans during the GlyTouCan project. WURCS defines rules for complex glycan structures that other text formats did not support, and so it is possible to represent a wide variety glycans. However, WURCS uses a complicated nomenclature, so it is not human-readable. Therefore, we aimed to support the interpretation of WURCS by converting WURCS to the most basic and widely used format IUPAC. Results In this study, we developed GlycanFormatConverter and succeeded in converting WURCS to the three kinds of IUPAC formats (IUPAC-Extended, IUPAC-Condensed and IUPAC-Short). Furthermore, we have implemented functionality to import IUPAC-Extended, KEGG Chemical Function (KCF) and LinearCode formats and to export WURCS. We have thoroughly tested our GlycanFormatConverter and were able to show that it was possible to convert all the glycans registered in the GlyTouCan repository, with exceptions owing only to the limitations of the original format. The source code for this conversion tool has been released as an open source tool. Availability and implementation https://github.com/glycoinfo/GlycanFormatConverter.git Supplementary information Supplementary data are available at Bioinformatics online.

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Hebert, Daniel N., Scott C. Garman, and Maurizio Molinari. "The glycan code of the endoplasmic reticulum: asparagine-linked carbohydrates as protein maturation and quality-control tags." Trends in Cell Biology 15, no. 7 (July 2005): 364–70. http://dx.doi.org/10.1016/j.tcb.2005.05.007.

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Lameignere, Emilie, Lenka Malinovská, Margita Sláviková, Eric Duchaud, Edward P. Mitchell, Annabelle Varrot, Ondrej Šedo, Anne Imberty, and Michaela Wimmerová. "Structural basis for mannose recognition by a lectin from opportunistic bacteria Burkholderia cenocepacia." Biochemical Journal 411, no. 2 (March 27, 2008): 307–18. http://dx.doi.org/10.1042/bj20071276.

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Chronic colonization of the lungs by opportunist bacteria such as Pseudomonas aeruginosa and members of the Bcc (Burkholderia cepacia complex) is the major cause of morbidity and mortality among CF (cystic fibrosis) patients. PA-IIL (lecB gene), a soluble lectin from Ps. aeruginosa, has been the subject of much interest because of its very strong affinity for fucose. Orthologues have been identified in the opportunist bacteria Ralstonia solanacearum, Chromobacterium violaceum and Burkholderia of Bcc. The genome of the J2315 strain of B. cenocepacia, responsible for epidemia in CF centres, contains three genes that code for proteins with PA-IIL domains. The shortest gene was cloned in Escherichia coli and pure recombinant protein, BclA (B. cenocepacia lectin A), was obtained. The presence of native BclA in B. cenocepacia extracts was checked using a proteomic approach. The specificity of recombinant BclA was characterized using surface plasmon resonance showing a preference for mannosides and supported with glycan array experiments demonstrating a strict specificity for oligomannose-type N-glycan structures. The interaction thermodynamics of BclA with methyl α-D-mannoside demonstrates a dissociation constant (Kd) of 2.75×10−6 M. The X-ray crystal structure of the complex with methyl α-D-mannoside was determined at 1.7 Å (1 Å=0.1 nm) resolution. The lectin forms homodimers with one binding site per monomer, acting co-operatively with the second dimer site. Each monomer contains two Ca2+ ions and one sugar ligand. Despite strong sequence similarity, the differences between BclA and PA-IIL in their specificity, binding site and oligomerization mode indicate that the proteins should have different roles in the bacteria.

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Neelamegham, Sriram, Kiyoko Aoki-Kinoshita, Evan Bolton, Martin Frank, Frederique Lisacek, Thomas Lütteke, Noel O’Boyle, et al. "Updates to the Symbol Nomenclature for Glycans guidelines." Glycobiology 29, no. 9 (June 11, 2019): 620–24. http://dx.doi.org/10.1093/glycob/cwz045.

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Abstract The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard for the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It is hosted by the National Center for Biotechnology Information (NCBI) at the NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to the SNFG page in the past year to update the rules for depicting glycans using the SNFG, to include more examples of use, particularly for non-mammalian organisms, and to provide guidelines for the depiction of ambiguous glycan structures. This Glycoforum article summarizes these recent changes.

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Noel, Eric, Anna Notaro, Immacolata Speciale, Garry A. Duncan, Cristina De Castro, and James L. Van Etten. "Chlorovirus PBCV-1 Multidomain Protein A111/114R Has Three Glycosyltransferase Functions Involved in the Synthesis of Atypical N-Glycans." Viruses 13, no. 1 (January 10, 2021): 87. http://dx.doi.org/10.3390/v13010087.

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The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of genetic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence analysis and protein modeling, we measured the hydrolytic activity of protein A111/114R. The results suggest that domain 1 is a galactosyltransferase, domain 2 is a xylosyltransferase and domain 3 is a fucosyltransferase. Thus, A111/114R is the protein likely responsible for the attachment of three of the five conserved residues of the core region of this complex glycan, and, if biochemically corroborated, it would be the second three-domain protein coded by PBCV-1 that is involved in glycan synthesis. Importantly, these findings provide additional support that the chloroviruses do not use the canonical host endoplasmic reticulum–Golgi glycosylation pathway to glycosylate their glycoproteins; instead, they perform glycosylation independent of cellular organelles using virus-encoded enzymes.

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Noel, Eric, Anna Notaro, Immacolata Speciale, Garry A. Duncan, Cristina De Castro, and James L. Van Etten. "Chlorovirus PBCV-1 Multidomain Protein A111/114R Has Three Glycosyltransferase Functions Involved in the Synthesis of Atypical N-Glycans." Viruses 13, no. 1 (January 10, 2021): 87. http://dx.doi.org/10.3390/v13010087.

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The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of genetic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence analysis and protein modeling, we measured the hydrolytic activity of protein A111/114R. The results suggest that domain 1 is a galactosyltransferase, domain 2 is a xylosyltransferase and domain 3 is a fucosyltransferase. Thus, A111/114R is the protein likely responsible for the attachment of three of the five conserved residues of the core region of this complex glycan, and, if biochemically corroborated, it would be the second three-domain protein coded by PBCV-1 that is involved in glycan synthesis. Importantly, these findings provide additional support that the chloroviruses do not use the canonical host endoplasmic reticulum–Golgi glycosylation pathway to glycosylate their glycoproteins; instead, they perform glycosylation independent of cellular organelles using virus-encoded enzymes.

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Biskup, Karina, Véronique Blanchard, Paola Castillo-Binder, Henry Alexander, Kurt Engeland, and Sindy Schug. "N- and O-glycosylation patterns and functional testing of CGB7 versus CGB3/5/8 variants of the human chorionic gonadotropin (hCG) beta subunit." Glycoconjugate Journal 37, no. 5 (August 7, 2020): 599–610. http://dx.doi.org/10.1007/s10719-020-09936-w.

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Abstract The classical function of human chorionic gonadotropin (hCG) is its role in supporting pregnancy. hCG is a dimer consisting of two highly glycosylated subunits, alpha (CGA) and beta (CGB). The beta-hCG protein is encoded by CGB3, CGB5, CGB7 and CGB8 genes. CGB3, 5 and 8 code for an identical protein, CGB3/5/8, whereas CGB7 differs in three amino acids from CGB3/5/8. We had observed earlier that CGB7 and CGB3/5/8 display very distinct tissue expression patterns and that the tumor suppressor and transcription factor p53 can activate expression of CGB7 but not of CGB3/5/8 genes. Here, we investigate the glycan structures and possible functional differences of the two CGB variants. To this end, we established a system to produce and isolate recombinant CGA, CGB7 and CGB3/5/8 proteins. We found that N- and O-glycosylation patterns of CGB7 and CGB3/5/8 are quite similar. Functional assays were performed by testing activation of the ERK1/2 pathway and demonstrated that CGB7 and CGB5/5/8 appear to be functionally redundant isoforms, although a slight difference in the kinetics of ERK1/2 pathway activation was observed. This is the first time that biological activity of CGB7 is shown. In summary, the results lead to the hypothesis that CGB7 and CGB3/5/8 do not hold significant functional differences but that timing and cell type of their expression is the key for understanding their divergent evolution.

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Sobral, Daniel, Rita Francisco, Laura Duro, Paula Alexandra Videira, and Ana Rita Grosso. "Concerted Regulation of Glycosylation Factors Sustains Tissue Identity and Function." Biomedicines 10, no. 8 (July 27, 2022): 1805. http://dx.doi.org/10.3390/biomedicines10081805.

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Glycosylation is a fundamental cellular process affecting human development and health. Complex machinery establishes the glycan structures whose heterogeneity provides greater structural diversity than other post-translational modifications. Although known to present spatial and temporal diversity, the evolution of glycosylation and its role at the tissue-specific level is poorly understood. In this study, we combined genome and transcriptome profiles of healthy and diseased tissues to uncover novel insights into the complex role of glycosylation in humans. We constructed a catalogue of human glycosylation factors, including transferases, hydrolases and other genes directly involved in glycosylation. These were categorized as involved in N-, O- and lipid-linked glycosylation, glypiation, and glycosaminoglycan synthesis. Our data showed that these glycosylation factors constitute an ancient family of genes, where evolutionary constraints suppressed large gene duplications, except for genes involved in O-linked and lipid glycosylation. The transcriptome profiles of 30 healthy human tissues revealed tissue-specific expression patterns preserved across mammals. In addition, clusters of tightly co-expressed genes suggest a glycosylation code underlying tissue identity. Interestingly, several glycosylation factors showed tissue-specific profiles varying with age, suggesting a role in ageing-related disorders. In cancer, our analysis revealed that glycosylation factors are highly perturbed, at the genome and transcriptome levels, with a strong predominance of copy number alterations. Moreover, glycosylation factor dysregulation was associated with distinct cellular compositions of the tumor microenvironment, reinforcing the impact of glycosylation in modulating the immune system. Overall, this work provides genome-wide evidence that the glycosylation machinery is tightly regulated in healthy tissues and impaired in ageing and tumorigenesis, unveiling novel potential roles as prognostic biomarkers or therapeutic targets.

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Gabius, Hans-Joachim. "The sugar code: Why glycans are so important." Biosystems 164 (February 2018): 102–11. http://dx.doi.org/10.1016/j.biosystems.2017.07.003.

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Yan, Maomao, Yuyang Zhu, Xueyun Liu, Yi Lasanajak, Jinglin Xiong, Jingqiao Lu, Xi Lin, et al. "Next-Generation Glycan Microarray Enabled by DNA-Coded Glycan Library and Next-Generation Sequencing Technology." Analytical Chemistry 91, no. 14 (June 12, 2019): 9221–28. http://dx.doi.org/10.1021/acs.analchem.9b01988.

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Zemkollari, Marilica, Markus Blaukopf, Reingard Grabherr, and Erika Staudacher. "Expression and Characterisation of the First Snail-Derived UDP-Gal: Glycoprotein-N-acetylgalactosamine β-1,3-Galactosyltransferase (T-Synthase) from Biomphalaria glabrata." Molecules 28, no. 2 (January 5, 2023): 552. http://dx.doi.org/10.3390/molecules28020552.

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UDP-Gal: glycoprotein-N-acetylgalactosamine β-1,3-galactosyltransferase (T-synthase, EC 2.4.1.122) catalyses the transfer of the monosaccharide galactose from UDP-Gal to GalNAc-Ser/Thr, synthesizing the core 1 mucin type O-glycan. Such glycans play important biological roles in a number of recognition processes. The crucial role of these glycans is acknowledged for mammals, but a lot remains unknown regarding invertebrate and especially mollusc O-glycosylation. Although core O-glycans have been found in snails, no core 1 β-1,3-galactosyltransferase has been described so far. Here, the sequence of the enzyme was identified by a BlastP search of the NCBI Biomphalaria glabrata database using the human T-synthase sequence (NP_064541.1) as a template. The obtained gene codes for a 388 amino acids long transmembrane protein with two putative N-glycosylation sites. The coding sequence was synthesised and expressed in Sf9 cells. The expression product of the putative enzyme displayed core 1 β-1,3-galactosyltransferase activity using pNP-α-GalNAc as the substrate. The enzyme showed some sequence homology (49.40% with Homo sapiens, 53.69% with Drosophila melanogaster and 49.14% with Caenorhabditis elegans) and similar biochemical parameters with previously characterized T-synthases from other phyla. In this study we present the identification, expression and characterisation of the UDP-Gal: glycoprotein-N-acetylgalactosamine β-1,3-galactosyltransferase from the fresh-water snail Biomphalaria glabrata, which is the first cloned T-synthase from mollusc origin.

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Nahalka, Jozef, Eva Hrabarova, and Klaudia Talafova. "Protein–RNA and protein–glycan recognitions in light of amino acid codes." Biochimica et Biophysica Acta (BBA) - General Subjects 1850, no. 9 (September 2015): 1942–52. http://dx.doi.org/10.1016/j.bbagen.2015.06.013.

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Leonti, Amanda R., Laura Pardo, Todd A. Alonzo, Robert B. Gerbing, Lisa Eidenschink Brodersen, Rhonda E. Ries, Jenny L. Smith, et al. "Transcriptome Profiling of Glycosylation Genes Defines Correlation with E-Selectin Ligand Expression and Clinical Outcome in AML." Blood 134, Supplement_1 (November 13, 2019): 3772. http://dx.doi.org/10.1182/blood-2019-124525.

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E-selectin (E-sel) is a cell adhesion glycoprotein that is expressed on endothelial cells and has been implicated in therapeutic resistance. In most myeloid leukemias, leukemic blasts express E-sel ligands (EsL), which contain the glycan epitope of the carbohydrate sialyl Lex (sLex). This expression increases the likelihood of adhesion to vascular endothelial cells and facilitates sequestration in the bone marrow vascular niche, leading to cell adhesion-mediated drug resistance and poor clinical outcome. E-sel antagonists like uproleselan, interrupts leukemic cell homing to the vascular niche, increases susceptibility to cytotoxic and targeted therapies and can be potent adjuncts to therapeutics. Recent data demonstrated a correlation between leukemic cell surface levels of EsL and response to uproleselan, linking EsL expression to response. We questioned whether transcriptome profiling of EsL-forming glycosylation genes can be used to identify elevated EsL expression in patients with acute myeloid leukemia (AML), and subsequently which patients might best respond to uproleselan. RNA-seq data from patients treated in COG AAML1031 (N = 1,074) was available for evaluation. We examined transcriptome expression of 24 genes that code for enzymes involved in glycosylation of EsL. All analyses were performed in R. Cox proportional hazards models were generated using the survival package. Multidimensional flow cytometry (MDF) was used to detect cell surface EsL expression by two techniques: direct binding of an E-sel/hIg, PE labeled chimera, and the anti-sLex antibody HECA-452. Seven of the 24 genes examined had minimal expression (mean <1 TPM) and were excluded from further analysis. The remaining 17 were variably expressed (Fig. 1A). To assess association of expression with outcome, univariate Cox models for overall survival (OS) were generated, using gene expression as a continuous coefficient (N = 1,061). Of the 17 genes, 7 were significantly associated with increased risk (p < 0.05, Fig. 1B). ST3GAL4 and FUT7 were targeted for further evaluation, as they directly synthesize sLex (Fig. 1C), and were significantly associated with adverse outcome (HR = 1.013, p < 0.0001, and HR = 1.023, p < 0.0001, respectively). Patients highly expressing FUT7 (highest quartile of expression) had significantly worse outcome than low expressors (lowest 3 quartiles of expression), with a 5-year OS of 50.3% vs. 68.3% (p < 0.0001, Fig. 1D). Similarly, those with high ST3GAL4 expression had a 5-year OS of 51.3%, compared to 68.1% for low expressors (p < 0.0001, Fig. 1D). A subset of patients highly expressed both genes (ST3GAL4 and FUT7 high; SFhigh, N = 132). Compared to patients that did not highly express either gene (SFlow), these individuals had particularly adverse survival (45.8% OS vs 71.0% OS, p < 0.0001). Patients with one of two high expressing genes (SFinter) had a 5-year OS of 55.5%, illustrating what may be a compounding unfavorable impact conferred on survival (Fig. 1E). Further investigation of clinical characteristics within these 3 groups revealed that 71.5% of infants <1 year were SFlow, with only 4.66% in SFhigh. In addition, CBF-AML was greatly underrepresented in SFhigh, with 97% of both t(8;21) and inv(16) patients in SFlow, and 0% in SFhigh. To verify surface protein expression of the two genes, leukemic specimens from SFhigh patients (N = 10) and SFlow patients (N = 10) underwent cell surface expression evaluation of glycosylated EsL using two MDF assays. SFlow patients had low or undetectable levels of cell surface EsL by both assays, whereas SFhigh patients had significantly higher expression of EsL (p < 0.001, Fig. 1F). This suggests a strong correlation between transcriptome measurements of EsL glycosylation genes and cell surface glycosylation levels of EsL. In summary, we have shown that multiple genes involved in the glycan synthesis of EsLs are highly expressed in pediatric AML. Two of these genes, ST3GAL4 and FUT7, are associated with poor outcome. Additionally, high expression of these genes is detectable at the transcript level and associated with cell surface EsL expression. These genes provide novel targets for overcoming drug resistance induced by the tumor microenvironment, and lend support for the use of EsL glycosylation genes as predictive biomarkers. These data also confirm the importance of E-sel in disease progression in AML and its potential as a therapeutic target. Figure 1 Disclosures Pardo: Hematologics, Inc: Employment. Eidenschink Brodersen:Hematologics, Inc: Employment. Magnani:GlycoMimetics Inc: Employment, Equity Ownership. Fogler:GlycoMimetics Inc: Employment, Equity Ownership. Loken:Hematologics, Inc: Employment, Equity Ownership.

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Cai, Yan, Jing Jiao, Zhichao Bin, Ying Zhang, Pengyuan Yang, and Haojie Lu. "Glycan reductive isotope-coded amino acid labeling (GRIAL) for mass spectrometry-based quantitative N-glycomics." Chemical Communications 51, no. 4 (2015): 772–75. http://dx.doi.org/10.1039/c4cc08086f.

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Hoja-Łukowicz, Dorota, Małgorzata Przybyło, Małgorzata Duda, Ewa Pocheć, and Monika Bubka. "On the trail of the glycan codes stored in cancer-related cell adhesion proteins." Biochimica et Biophysica Acta (BBA) - General Subjects 1861, no. 1 (January 2017): 3237–57. http://dx.doi.org/10.1016/j.bbagen.2016.08.007.

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Moll, Markus, Andreas Kaufmann, and Andrea Maisner. "Influence of N-Glycans on Processing and Biological Activity of the Nipah Virus Fusion Protein." Journal of Virology 78, no. 13 (July 1, 2004): 7274–78. http://dx.doi.org/10.1128/jvi.78.13.7274-7278.2004.

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ABSTRACT Nipah virus (NiV), a new member of the Paramyxoviridae, codes for a fusion (F) protein with five potential N-glycosylation sites. Because glycans are known to be important structural components affecting the conformation and function of viral glycoproteins, we analyzed the effect of the deletion of N-linked oligosaccharides on cell surface transport, proteolytic cleavage, and the biological activity of the NiV F protein. Each of the five potential glycosylation sites was removed either individually or in combination, revealing that four sites are actually utilized (g2 and g3 in the F2 subunit and g4 and g5 in the F1 subunit). While the removal of g2 and/or g3 had no or little effect on cleavage, surface transport, and fusion activity, the elimination of g4 or g5 reduced the surface expression by more than 80%. Similar to a mutant lacking all N-glycans, g4 deletion mutants in which the potential glycosylation site was destroyed by introducing a glycine residue were neither cleaved nor transported to the cell surface and consequently were not able to mediate cell-to-cell fusion. This finding indicates that in the absence of g4, the amino acid sequence around position 414 is important for folding and transport.

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Amthauer, R., K. Kodukula, and S. Udenfriend. "Placental Alkaline Phosphatase: A Model for Studying COOH-Terminal Processing of Phosphatidylinositol-Glycan-Anchored Membrane Proteins." Clinical Chemistry 38, no. 12 (December 1, 1992): 2510–16. http://dx.doi.org/10.1093/clinchem/38.12.2510.

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Abstract Placental alkaline phosphatase (PLAP) has been used as a model for studying the biosynthesis of the phosphatidylinositol-glycan (PI-G)-protein linkage in intact cells and in cell-free systems. However, for the study of processing in cell-free systems, a small protein devoid of glycosylation sites is preferable. A PLAP-derived cDNA was engineered that codes for a nascent protein (mini-PLAP) of 28 kDa in which the NH2- and COOH-termini are retained but most of the interior of PLAP is deleted. In vitro translation of mini-PLAP mRNA in the presence of rough microsomal membranes yields mature PI-G-tailed mini-PLAP. Processing of nascent mutant proteins occurs only when a small amino acid is located at the site of cleavage and PI-G attachment (omega site). Mutations adjacent and COOH-terminal to the omega site have revealed that the omega + 1 site is promiscuous in its requirements but that only glycine and alanine are effective at the omega + 2 site. Rough microsomal membranes from T cells deficient in PI-G biosynthesis do not support processing of mini-PLAP; addition of exogenous PI-G restores activity. Translocation of the proprotein, most likely requiring ATP and GTP, precedes COOH-terminal processing.

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Beckwith, Donella M., and Maré Cudic. "Tumor-associated O-glycans of MUC1: Carriers of the glyco-code and targets for cancer vaccine design." Seminars in Immunology 47 (February 2020): 101389. http://dx.doi.org/10.1016/j.smim.2020.101389.

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Lei, Lei, and Zachary F. Burton. "Evolution of Life on Earth: tRNA, Aminoacyl-tRNA Synthetases and the Genetic Code." Life 10, no. 3 (March 2, 2020): 21. http://dx.doi.org/10.3390/life10030021.

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Life on Earth and the genetic code evolved around tRNA and the tRNA anticodon. We posit that the genetic code initially evolved to synthesize polyglycine as a cross-linking agent to stabilize protocells. We posit that the initial amino acids to enter the code occupied larger sectors of the code that were then invaded by incoming amino acids. Displacements of amino acids follow selection rules. The code sectored from a glycine code to a four amino acid code to an eight amino acid code to an ~16 amino acid code to the standard 20 amino acid code with stops. The proposed patterns of code sectoring are now most apparent from patterns of aminoacyl-tRNA synthetase evolution. The Elongation Factor-Tu GTPase anticodon-codon latch that checks the accuracy of translation appears to have evolved at about the eight amino acid to ~16 amino acid stage. Before evolution of the EF-Tu latch, we posit that both the 1st and 3rd anticodon positions were wobble positions. The genetic code evolved via tRNA charging errors and via enzymatic modifications of amino acids joined to tRNAs, followed by tRNA and aminoacyl-tRNA synthetase differentiation. Fidelity mechanisms froze the code by inhibiting further innovation.

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Xu, Jianfeng, Li Tan, Derek T. A. Lamport, Allan M. Showalter, and Marcia J. Kieliszewski. "The O-Hyp glycosylation code in tobacco and Arabidopsis and a proposed role of Hyp-glycans in secretion." Phytochemistry 69, no. 8 (May 2008): 1631–40. http://dx.doi.org/10.1016/j.phytochem.2008.02.006.

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Wang, Yuying, Yan Cai, Ying Zhang, and Haojie Lu. "Glycan reductive amino acid coded affinity tagging (GRACAT) for highly specific analysis of N-glycome by mass spectrometry." Analytica Chimica Acta 1089 (December 2019): 90–99. http://dx.doi.org/10.1016/j.aca.2019.08.054.

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Inouye, Masayori, Risa Takino, Yojiro Ishida, and Keiko Inouye. "Evolution of the genetic code; Evidence from serine codon use disparity inEscherichia coli." Proceedings of the National Academy of Sciences 117, no. 46 (November 9, 2020): 28572–75. http://dx.doi.org/10.1073/pnas.2014567117.

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Among the 20 amino acids, three of them—leucine (Leu), arginine (Arg), and serine (Ser)—are encoded by six different codons. In comparison, all of the other 17 amino acids are encoded by either 4, 3, 2, or 1 codon. Peculiarly, Ser is separated into two disparate Ser codon boxes, differing by at least two-base substitutions, in contrast to Leu and Arg, of which codons are mutually exchangeable by a single-base substitution. We propose that these two different Ser codons independently emerged during evolution. In this hypothesis, at the time of the origin of life there were only seven primordial amino acids: Valine (coded by GUX [X = U, C, A or G]), alanine (coded by GCX), aspartic acid (coded by GAY [Y = U or C]), glutamic acid (coded by GAZ [Z = A or G]), glycine (coded by GGX), Ser (coded by AGY), and Arg (coded by CGX and AGZ). All of these were derived from GGX for glycine by single-base substitutions. Later in evolution, another class of Ser codons, UCX, were derived from alanine codons, GCX, distinctly different from the other primordial Ser codon, AGY. From the analysis of theEscherichia coligenome, we find extensive disparities in the usage of these two Ser codons, as some genes use only AGY for Ser in their genes. In contrast, others use only UCX, pointing to distinct differences in their origins, consistent with our hypothesis.

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Polikarpov, I., A. M. Golubev, L. A. Perles, S. C. Pando, J. C. Novello, and S. Marangoni. "Purification, crystallization and preliminary crystallographic study of a Kunitz-type trypsin inhibitor from Delonix regia seeds." Acta Crystallographica Section D Biological Crystallography 55, no. 9 (September 1, 1999): 1611–13. http://dx.doi.org/10.1107/s0907444999009361.

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The Kunitz-type trypsin inhibitor from seeds of Flamboyant (Delonix regia) has been purified to homogeneity and plate-like crystals suitable for X-ray analysis have been grown by the hanging-drop method using PEG 6000 as a precipitant. The crystals belong to space group P212121 with unit-cell parameters a = 32.15, b = 69.39, c = 72.54 Å. X-ray diffraction data have been collected to 2.95 Å resolution. The structure has been solved by molecular replacement using the known structures of trypsin inhibitors from Erythrina caffra seeds (PDB code 1tie) and from soya beans (Glycine max; PDB code 1ba7) as search models.

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Hartman, Hyman, and Temple F. Smith. "Origin of the Genetic Code Is Found at the Transition between a Thioester World of Peptides and the Phosphoester World of Polynucleotides." Life 9, no. 3 (August 22, 2019): 69. http://dx.doi.org/10.3390/life9030069.

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The early metabolism arising in a Thioester world gave rise to amino acids and their simple peptides. The catalytic activity of these early simple peptides became instrumental in the transition from Thioester World to a Phosphate World. This transition involved the appearances of sugar phosphates, nucleotides, and polynucleotides. The coupling of the amino acids and peptides to nucleotides and polynucleotides is the origin for the genetic code. Many of the key steps in this transition are seen in in the catalytic cores of the nucleotidyltransferases, the class II tRNA synthetases (aaRSs) and the CCA adding enzyme. These catalytic cores are dominated by simple beta hairpin structures formed in the Thioester World. The code evolved from a proto-tRNA a tetramer XCCA interacting with a proto-aminoacyl-tRNA synthetase (aaRS) activating Glycine and Proline, the initial expanded code is found in the acceptor arm of the tRNA, the operational code. It is the coevolution of the tRNA with the aaRSs that is at the heart of the origin and evolution of the genetic code. There is also a close relationship between the accretion models of the evolving tRNA and that of the ribosome.

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Duprez, Daniel A., James Otvos, Otto A. Sanchez, Rachel H. Mackey, Russell Tracy, and David R. Jacobs. "Comparison of the Predictive Value of GlycA and Other Biomarkers of Inflammation for Total Death, Incident Cardiovascular Events, Noncardiovascular and Noncancer Inflammatory-Related Events, and Total Cancer Events." Clinical Chemistry 62, no. 7 (July 1, 2016): 1020–31. http://dx.doi.org/10.1373/clinchem.2016.255828.

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Abstract BACKGROUND GlycA is a biomarker that reflects integrated concentrations and glycosylation states of several acute-phase proteins. We studied the association of GlycA and inflammatory biomarkers with future death and disease. METHODS A total of 6523 men and women in the Multi-Ethnic Study of Atherosclerosis who were free of overt cardiovascular disease (CVD) and in generally good health had a baseline blood sample taken. We assayed high-sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), and d-dimer. A spectral deconvolution algorithm was used to quantify GlycA signal amplitudes from automated nuclear magnetic resonance (NMR) LipoProfile® test spectra. Median follow-up was 12.1 years. Among 4 primary outcomes, CVD events were adjudicated, death was by death certificate, and chronic inflammatory-related severe hospitalization and death (ChrIRD) and total cancer were classified using International Classification of Diseases (ICD) codes. We used Poisson regression to study baseline GlycA, hsCRP, IL-6, and d-dimer in relation to total death, CVD, ChrIRD, and total cancer. RESULTS Relative risk per SD of GlycA, IL-6, and d-dimer for total death (n = 915); for total CVD (n = 922); and for ChrIRD (n = 1324) ranged from 1.05 to 1.20, independently of covariates. In contrast, prediction from hsCRP was statistically explained by adjustment for other inflammatory variables. Only GlycA was predictive for total cancer (n = 663). Women had 7% higher values of all inflammatory biomarkers than men and had a significantly lower GlycA prediction coefficient than men in predicting total cancer. CONCLUSIONS The composite biomarker GlycA derived from NMR is associated with risk for total death, CVD, ChrIRD, and total cancer after adjustment for hsCRP, IL-6, and d-dimer. IL-6 and d-dimer contribute information independently of GlycA.

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Pichon, Julien, Nicholas M. Luscombe, and Charles Plessy. "Widespread use of the “ascidian” mitochondrial genetic code in tunicates." F1000Research 8 (December 10, 2019): 2072. http://dx.doi.org/10.12688/f1000research.21551.1.

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Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.

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Pichon, Julien, Nicholas M. Luscombe, and Charles Plessy. "Widespread use of the “ascidian” mitochondrial genetic code in tunicates." F1000Research 8 (April 14, 2020): 2072. http://dx.doi.org/10.12688/f1000research.21551.2.

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Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.

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Barceló-Antemate, Diana, Fernando Fontove-Herrera, Walter Santos, and Enrique Merino. "The effect of the genomic GC content bias of prokaryotic organisms on the secondary structures of their proteins." PLOS ONE 18, no. 5 (May 4, 2023): e0285201. http://dx.doi.org/10.1371/journal.pone.0285201.

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One of the main characteristics of prokaryotic genomes is the ratio in which guanine-cytosine bases are used in their DNA sequences. This is known as the genomic GC content and varies widely, from values below 20% to values greater than 74%. It has been demonstrated that the genomic GC content varies in accordance with the phylogenetic distribution of organisms and influences the amino acid composition of their corresponding proteomes. This bias is particularly important for amino acids that are coded by GC content-rich codons such as alanine, glycine, and proline, as well as amino acids that are coded by AT-rich codons, such as lysine, asparagine, and isoleucine. In our study, we extend these results by considering the effect of the genomic GC content on the secondary structure of proteins. On a set of 192 representative prokaryotic genomes and proteome sequences, we identified through a bioinformatic study that the composition of the secondary structures of the proteomes varies in relation to the genomic GC content; random coils increase as the genomic GC content increases, while alpha-helices and beta-sheets present an inverse relationship. In addition, we found that the tendency of an amino acid to form part of a secondary structure of proteins is not ubiquitous, as previously expected, but varies according to the genomic GC content. Finally, we discovered that for some specific groups of orthologous proteins, the GC content of genes biases the composition of secondary structures of the proteins for which they code.

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Kim, Yunsoo, Kristopher Opron, and Zachary F. Burton. "A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code." Life 9, no. 2 (May 4, 2019): 37. http://dx.doi.org/10.3390/life9020037.

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Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by sequence. Specifically, structural class IA aaRS enzymes derive from class IIA aaRS enzymes by in-frame extension of the protein N-terminus and by an alternate fold nucleated by the N-terminal extension. The divergence of aaRS enzymes in the class I and class II clades was analyzed using the Phyre2 protein fold recognition server. The class I aaRS radiated from the class IA enzymes, and the class II aaRS radiated from the class IIA enzymes. The radiations of aaRS enzymes bolster the coevolution theory for evolution of the amino acids, tRNAomes, the genetic code, and aaRS enzymes and support a tRNA anticodon-centric perspective. We posit that second- and third-position tRNA anticodon sequence preference (C>(U~G)>A) powerfully selected the sectoring pathway for the code. GlyRS-IIA appears to have been the primordial aaRS from which all aaRS enzymes evolved, and glycine appears to have been the primordial amino acid around which the genetic code evolved.

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Silflow, C. D., R. L. Chisholm, T. W. Conner, and L. P. Ranum. "The two alpha-tubulin genes of Chlamydomonas reinhardi code for slightly different proteins." Molecular and Cellular Biology 5, no. 9 (September 1985): 2389–98. http://dx.doi.org/10.1128/mcb.5.9.2389-2398.1985.

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Full-length cDNA clones corresponding to the transcripts of the two alpha-tubulin genes in Chlamydomonas reinhardi were isolated. DNA sequence analysis of the cDNA clones and cloned gene fragments showed that each gene contains 1,356 base pairs of coding sequence, predicting alpha-tubulin products of 451 amino acids. Of the 27 nucleotide differences between the two genes, only two result in predicted amino acid differences between the two gene products. In the more divergent alpha 2 gene, a leucine replaces an arginine at amino acid 308, and a valine replaces a glycine at amino acid 366. The results predicted that two alpha-tubulin proteins with different net charges are produced as primary gene products. The predicted amino acid sequences are 86 and 70% homologous with alpha-tubulins from rat brain and Schizosaccharomyces pombe, respectively. Each gene had two intervening sequences, located at identical positions. Portions of an intervening sequence highly conserved between the two beta-tubulin genes are also found in the second intervening sequence of each of the alpha genes. These results, together with our earlier report of the beta-tubulin sequences in C. reinhardi, present a picture of the total complement of genetic information for tubulin in this organism.

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Silflow, C. D., R. L. Chisholm, T. W. Conner, and L. P. Ranum. "The two alpha-tubulin genes of Chlamydomonas reinhardi code for slightly different proteins." Molecular and Cellular Biology 5, no. 9 (September 1985): 2389–98. http://dx.doi.org/10.1128/mcb.5.9.2389.

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Full-length cDNA clones corresponding to the transcripts of the two alpha-tubulin genes in Chlamydomonas reinhardi were isolated. DNA sequence analysis of the cDNA clones and cloned gene fragments showed that each gene contains 1,356 base pairs of coding sequence, predicting alpha-tubulin products of 451 amino acids. Of the 27 nucleotide differences between the two genes, only two result in predicted amino acid differences between the two gene products. In the more divergent alpha 2 gene, a leucine replaces an arginine at amino acid 308, and a valine replaces a glycine at amino acid 366. The results predicted that two alpha-tubulin proteins with different net charges are produced as primary gene products. The predicted amino acid sequences are 86 and 70% homologous with alpha-tubulins from rat brain and Schizosaccharomyces pombe, respectively. Each gene had two intervening sequences, located at identical positions. Portions of an intervening sequence highly conserved between the two beta-tubulin genes are also found in the second intervening sequence of each of the alpha genes. These results, together with our earlier report of the beta-tubulin sequences in C. reinhardi, present a picture of the total complement of genetic information for tubulin in this organism.

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Напалкова, Светлана Михайловна, and Ольга Владимировна Буюклинская. "EFFECT OF 1,4-NAPHTHOQUINONE ALKYLATED AMINO ACIDS DERIVATIVES ON CARDIOHEMODYNAMICS ON ISCHEMIC MYOCARDIUM MODEL." ВЕСТНИК ОБРАЗОВАНИЯ И РАЗВИТИЯ НАУКИ РОССИЙСКОЙ АКАДЕМИИ ЕСТЕСТВЕННЫХ НАУК, no. 4 (December 15, 2021): 66–71. http://dx.doi.org/10.26163/raen.2021.48.21.010.

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Изучалось влияние производных трех аминокислот (глицин, глютаминовая и аспарагиновая кислоты), алкилированных 1,4-нафтохиноном, на кардиогемодинамику на модели ишемизированного миокарда. Установлено, что все исследованные соединения (лабораторные шифры НХА, НХГ, НХГА) на модели ишемии миокарда, вызванной окклюзией коронарной артерии, предупреждали снижение сократимости сердечной мышцы. Производное глицина (НХГ) в большей степени предупреждало снижение уровня среднего артериального давления, тогда как наименее заметное влияние на этот показатель оказывало соединение с лабораторным шифром НХГК (производное глютаминовой кислоты). Влияние изучаемых соединений на частоту сердечных сокращений (ЧСС) неоднозначно зависело от времени наблюдения: НХГ в дозе 4 мг/кг предупреждало урежение ЧСС на 5 и 10 мин. регистрации, НХА (производное аспарагиновой кислоты) в дозе 5 мг/кг при внутривенном введении предупреждало урежение ЧСС на 20 и 30 мин. эксперимента, а НХГК в дозе 4 мг/кг предупреждало урежение ЧСС 30, 40 и 60 мин. We studied the effect of derivatives of three amino acids (glycine, glutamic and asparginic acids) alkylated with 1,4-naphthoquinone on cardiohemodynamics on the model of ischemic myocardium. We prove that thetested compounds (having the laboratory codes NHA, NHG, NHGA) in the model of myocardial ischemia caused by coronary artery occlusion prevented a decrease in the contractility of the heart muscle. The glycine derivative (NHG) prevented a the mean arterial pressure fall to a greater extent, while the least noticeable effect resulted from the compound with the laboratory code of NHGA (a derivative of glutamic acid). The effect of the compounds in question on the heart rate depended on the observation time:NHG in the dose of 4 mg/kg prevented the heart rate fall by 5 and 10 minutes of registration, NHA (a derivative of asparginic acid) in the dose of 5 mg/kg when administered intravenously prevented the heart rate fall for 20 and 30 minutes of the experiment, while NHGA in the dose of 4 mg / kg prevented the heart rate fall for 30, 40 and 60 minutes.

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Michael, Claudia, and Andreas M. Rizzi. "Quantitative isomer-specific N-glycan fingerprinting using isotope coded labeling and high performance liquid chromatography–electrospray ionization-mass spectrometry with graphitic carbon stationary phase." Journal of Chromatography A 1383 (February 2015): 88–95. http://dx.doi.org/10.1016/j.chroma.2015.01.028.

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Shu, Longfei, Jie Qiu, and Katja Räsänen. "De novo oviduct transcriptome of the moor frog Rana arvalis: a quest for maternal effect candidate genes." PeerJ 6 (August 16, 2018): e5452. http://dx.doi.org/10.7717/peerj.5452.

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Maternal effects can substantially affect ecological and evolutionary processes in natural populations. However, as they often are environmentally induced, establishing their genetic basis is challenging. One important, but largely neglected, source of maternal effects are egg coats (i.e., the maternally derived extracellular matrix that surrounds the embryo). In the moor frog, the gelatinous egg coats (i.e., egg jelly) are produced in the mother’s oviduct and consist primarily of highly glycosylated mucin type O-glycans. These O-glycans affect jelly water balance and, subsequently, contribute to adaptive divergence in embryonic acid tolerance. To identify candidate genes for maternal effects, we conducted RNAseq transcriptomics on oviduct samples from seven R. arvalis females, representing the full range of within and among population variation in embryonic acid stress tolerance across our study populations. De novo sequencing of these oviduct transcriptomes detected 124,071 unigenes and functional annotation analyses identified a total of 57,839 unigenes, of which several identified genes likely code for variation in egg jelly coats. These belonged to two main groups: mucin type core protein genes and five different types of glycosylation genes. We further predict 26,711 gene-linked microsatellite (simple sequence repeats) and 231,274 single nucleotide polymorphisms. Our study provides the first set of genomic resources for R. arvalis, an emerging model system for the study of ecology and evolution in natural populations, and gives insight into the genetic architecture of egg coat mediated maternal effects.

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Ribeiro, João P., William Pau, Carlo Pifferi, Olivier Renaudet, Annabelle Varrot, Lara K. Mahal, and Anne Imberty. "Characterization of a high-affinity sialic acid-specific CBM40 from Clostridium perfringens and engineering of a divalent form." Biochemical Journal 473, no. 14 (July 12, 2016): 2109–18. http://dx.doi.org/10.1042/bcj20160340.

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CBMs (carbohydrate-binding modules) are a class of polypeptides usually associated with carbohydrate-active enzymatic sites. We have characterized a new member of the CBM40 family, coded from a section of the gene NanI from Clostridium perfringens. Glycan arrays revealed its preference towards α(2,3)-linked sialosides, which was confirmed and quantified by calorimetric studies. The CBM40 binds to α(2,3)-sialyl-lactose with a Kd of ∼30 μM, the highest affinity value for this class of proteins. Inspired by lectins' structure and their arrangement as multimeric proteins, we have engineered a dimeric form of the CBM, and using SPR (surface plasmon resonance) we have observed 6–11-fold binding increases due to the avidity affect. The structures of the CBM, resolved by X-ray crystallography, in complex with α(2,3)- or α(2,6)-sialyl-lactose explain its binding specificity and unusually strong binding.

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Nawaz, Muhammad Amjad, Xiao Lin, Ting-Fung Chan, Junghee Ham, Tai-Sun Shin, Sezai Ercisli, Kirill S. Golokhvast, Hon-Ming Lam, and Gyuhwa Chung. "Korean Wild Soybeans (Glycine soja Sieb & Zucc.): Geographic Distribution and Germplasm Conservation." Agronomy 10, no. 2 (February 2, 2020): 214. http://dx.doi.org/10.3390/agronomy10020214.

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Domesticated crops suffer from major genetic bottlenecks while wild relatives retain higher genomic diversity. Wild soybean (Glycine soja Sieb. & Zucc.) is the presumed ancestor of cultivated soybean (Glycine max [L.] Merr.), and is an important genetic resource for soybean improvement. Among the East Asian habitats of wild soybean (China, Japan, Korea, and Northeastern Russia), the Korean peninsula is of great importance based on archaeological records, domestication history, and higher diversity of wild soybeans in the region. The collection and conservation of these wild soybean germplasms should be put on high priority. Chung’s Wild Legume Germplasm Collection maintains more than 10,000 legume accessions with an intensive and prioritized wild soybean germplasm collection (>6000 accessions) guided by the international code of conduct for plant germplasm collection and transfer. The center holds a library of unique wild soybean germplasms collected from East Asian wild habitats including the Korean mainland and nearby islands. The collection has revealed interesting and useful morphological, biochemical, and genetic diversity. This resource could be utilized efficiently in ongoing soybean improvement programs across the globe.

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Journal articles on the topic 'Glycan code'

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