scholarly journals A library of structurally homogeneous human N-glycans synthesized from microbial oligosaccharide precursors

2017 ◽  
Author(s):  
Brian S. Hamilton ◽  
Joshua D. Wilson ◽  
Marina A. Shumakovich ◽  
Adam C. Fisher ◽  
James C. Brooks ◽  
...  
Keyword(s):  
Enzymatic Method ◽  
Molecular Tools ◽  
Wild Type ◽  
Complex Type ◽  
Purification Scheme ◽  
Major Bottleneck ◽  
Health And Disease ◽  
Glycosylation Pathway ◽  
User Friendly ◽  
Oligosaccharide Structures

AbstractSynthesis of homogenous glycans in quantitative yields represents a major bottleneck to the production of molecular tools for glycoscience, such as glycan microarrays, affinity resins, and reference standards. Here, we describe a combined biological/enzymatic method termed bioenzymatic synthesis that is capable of efficiently converting microbially-derived precursor oligosaccharides into structurally uniform human-type N-glycans. Unlike starting material obtained by chemical synthesis or direct isolation from natural sources, which can be time consuming and costly to generate, bioenzymatic synthesis involves precursors derived from renewable sources including wild-type Saccharomyces cerevisiae glycoproteins and lipid-linked oligosaccharides from glycoengineered Escherichia coli. Following deglycosylation of these biosynthetic precursors, the resulting microbial oligosaccharides are subjected to a greatly simplified purification scheme followed by structural remodeling using commercially available and recombinantly produced glycosyltransferases including key N- acetylglucosaminyltransferases (e.g., GnTI, GnTII, and GnTIV) involved in early remodeling of glycans in the mammalian glycosylation pathway. Using this approach, preparative quantities of hybrid and complex-type N-glycans including asymmetric multi-antennary structures were generated all without the need of a specialized skillset. Collectively, our results reveal bioenzymatic synthesis to be a user-friendly methodology for rapidly supplying homogeneous oligosaccharide structures that can be used to understand the human glycome and probe the biological roles of glycans in health and disease.

scholarly journals Multiplexed engineering glycosyltransferase genes in CHO cells via targeted integration for producing antibodies with diverse complex-type N-glycans

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ngan T. B. Nguyen ◽  
Jianer Lin ◽  
Shi Jie Tay ◽  
Mariati ◽  
Jessna Yeo ◽  
...  
Keyword(s):  
Cho Cells ◽  
Structure And Function ◽  
Glycan Structure ◽  
Wild Type ◽  
Complex Type ◽  
Cassette Exchange ◽  
Glycosylation Pathway ◽  
And Function ◽  
First Time ◽  
Gene Expression Levels

AbstractTherapeutic antibodies are decorated with complex-type N-glycans that significantly affect their biodistribution and bioactivity. The N-glycan structures on antibodies are incompletely processed in wild-type CHO cells due to their limited glycosylation capacity. To improve N-glycan processing, glycosyltransferase genes have been traditionally overexpressed in CHO cells to engineer the cellular N-glycosylation pathway by using random integration, which is often associated with large clonal variations in gene expression levels. In order to minimize the clonal variations, we used recombinase-mediated-cassette-exchange (RMCE) technology to overexpress a panel of 42 human glycosyltransferase genes to screen their impact on antibody N-linked glycosylation. The bottlenecks in the N-glycosylation pathway were identified and then released by overexpressing single or multiple critical genes. Overexpressing B4GalT1 gene alone in the CHO cells produced antibodies with more than 80% galactosylated bi-antennary N-glycans. Combinatorial overexpression of B4GalT1 and ST6Gal1 produced antibodies containing more than 70% sialylated bi-antennary N-glycans. In addition, antibodies with various tri-antennary N-glycans were obtained for the first time by overexpressing MGAT5 alone or in combination with B4GalT1 and ST6Gal1. The various N-glycan structures and the method for producing them in this work provide opportunities to study the glycan structure-and-function and develop novel recombinant antibodies for addressing different therapeutic applications.

Targeted deletion of murine coagulation factor XII gene-a model for contact phase activation in vivo

2004 ◽  
Vol 92 (09) ◽  
pp. 503-508 ◽  
Author(s):  
Hans-Ulrich Pauer ◽  
Thomas Renné ◽  
Bernhard Hemmerlein ◽  
Tobias Legler ◽  
Saskia Fritzlar ◽  
...  
Keyword(s):  
Fetal Loss ◽  
Coagulation Factor ◽  
Coagulation Factors ◽  
Mendelian Inheritance ◽  
Biological Role ◽  
Factor Xii ◽  
Wild Type ◽  
Contact Phase ◽  
Health And Disease

SummaryTo analyze the biological role of factor XII (FXII, Hageman Factor) in vivo, we generated mice deficient for FXII using a gene targeting approach on two distinct genetic backgrounds, i.e. mixed C57Bl/6J X 129X1/SvJ and inbred 129X1/SvJ. Homozygous FXII knockout (FXII-/-) mice showed no FXII plasma activity and had a markedly prolonged activated partial thromboplastin time (aPTT). In contrast, coagulation factors XI, VIII, IX, X,VII,V, II and fibrinogen did not differ between FXII-/- mice and their wild-type littermates. Heterozygous matings segregated according to the Mendelian inheritance indicating that FXII deficiency does not increase fetal loss. Furthermore, matings of FXII-/- males and FXII-/females resulted in normal litter sizes demonstrating that total FXII deficiency in FXII-/females does not affect pregnancy outcome. Also, gross and histological anatomy of FXII-/mice was indistinguishable from that of their wild-type littermates on both genetic backgrounds. Thus it appears that deficiency of murine FXII does not cause thrombophilia or impaired fibrinolysis in vivo. These results indicate that FXII deficiency does not affect hemostasis in vivo and we anticipate that the FXII-/mice will be helpful to elucidate the biological role(s) of FXII in health and disease.

A novel enzymatic method for synthesis of glycopeptides carrying natural eukaryotic N-glycans

2017 ◽  
Vol 53 (65) ◽  
pp. 9075-9077 ◽  
Author(s):  
Yangyang Xu ◽  
Zhigang Wu ◽  
Peiru Zhang ◽  
He Zhu ◽  
Hailiang Zhu ◽  
...  
Keyword(s):  
Enzymatic Reactions ◽  
Enzymatic Method ◽  
Complex Type

Production of glycopeptides carrying complex-type N-glycans via three steps of enzymatic reactions.

scholarly journals Deletions into an NH2-terminal hydrophobic domain result in secretion of rotavirus VP7, a resident endoplasmic reticulum membrane glycoprotein.

1985 ◽  
Vol 101 (6) ◽  
pp. 2199-2209 ◽  
Author(s):  
M S Poruchynsky ◽  
C Tyndall ◽  
G W Both ◽  
F Sato ◽  
A R Bellamy ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Integral Membrane Protein ◽  
Endoplasmic Reticulum Membrane ◽  
Wild Type ◽  
Positive Signal ◽  
Complex Type ◽  
Immunofluorescent Localization ◽  
Hydrophobic Domain ◽  
Rotavirus A ◽  
Altered Protein

Rotavirus, a non-enveloped reovirus, buds into the rough endoplasmic reticulum and transiently acquires a membrane. The structural glycoprotein, VP7, a 38-kD integral membrane protein of the endoplasmic reticulum (ER), presumably transfers to virus in this process. The gene for VP7 potentially encodes a protein of 326 amino acids which has two tandem hydrophobic domains at the NH2-terminal, each preceded by an in-frame ATG codon. A series of deletion mutants constructed from a full-length cDNA clone of the Simian 11 rotavirus VP7 gene were expressed in COS 7 cells. Products from wild-type, and mutants which did not affect the second hydrophobic domain of VP7, were localized by immunofluorescence to elements of the ER only. However, deletions affecting the second hydrophobic domain (mutants 42-61, 43-61, 47-61) showed immunofluorescent localization of VP7 which coincided with that of wheat germ agglutinin, indicating transport to the Golgi apparatus. Immunoprecipitable wild-type protein, or an altered protein lacking the first hydrophobic sequence, remained intracellular and endo-beta-N-acetylglucosaminidase H sensitive. In contrast, products of mutants 42-61, 43-61, and 47-61 were transported from the ER, and secreted. Glycosylation of the secreted molecules was inhibited by tunicamycin, resistant to endo-beta-N-acetylglucosaminidase H digestion and therefore of the N-linked complex type. An unglycosylated version of VP7 was also secreted. We suggest that the second hydrophobic domain contributes to a positive signal for ER location and a membrane anchor function. Secretion of the mutant glycoprotein implies that transport can be constitutive with the destination being dictated by an overriding compartmentalization signal.

scholarly journals Tetherin is an exosomal tether

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
James R Edgar ◽  
Paul T Manna ◽  
Shinichi Nishimura ◽  
George Banting ◽  
Margaret S Robinson
Keyword(s):  
Plasma Membrane ◽  
Cell Surface ◽  
Short Range ◽  
Wild Type ◽  
Concomitant Increase ◽  
Gpi Anchor ◽  
Fold Reduction ◽  
Cell Metastasis ◽  
Health And Disease ◽  
Prion Transmission

Exosomes are extracellular vesicles that are released when endosomes fuse with the plasma membrane. They have been implicated in various functions in both health and disease, including intercellular communication, antigen presentation, prion transmission, and tumour cell metastasis. Here we show that inactivating the vacuolar ATPase in HeLa cells causes a dramatic increase in the production of exosomes, which display endocytosed tracers, cholesterol, and CD63. The exosomes remain clustered on the cell surface, similar to retroviruses, which are attached to the plasma membrane by tetherin. To determine whether tetherin also attaches exosomes, we knocked it out and found a 4-fold reduction in plasma membrane-associated exosomes, with a concomitant increase in exosomes discharged into the medium. This phenotype could be rescued by wild-type tetherin but not tetherin lacking its GPI anchor. We propose that tetherin may play a key role in exosome fate, determining whether they participate in long-range or short-range interactions.

scholarly journals A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Simon Roux
Keyword(s):  
Cell Metabolism ◽  
Ecosystem Functions ◽  
Biological Knowledge ◽  
Viral Sequence ◽  
Molecular Tools ◽  
Microbial Cells ◽  
Health And Disease ◽  
Virus Genomes ◽  
Do So

ABSTRACTMicrobes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection. While the majority of viruses and their associated impacts remain poorly characterized, a number of mechanisms by which viruses alter microbial cells and ecosystems have already been revealed. Here I outline how a comprehensive host-resolved mapping of viral sequence space will enable a thorough characterization of virus-encoded mechanisms for microbial manipulation. With soon-to-be millions of virus genomes obtained from metagenomes, one of the major challenges resides in the development of methods for high-throughput and high-resolution virus-host pairing, before multi-omics approaches can be leveraged to fully decipher virus-host dynamics in nature. Beyond novel fundamental biological knowledge, these studies will likely provide new molecular tools enabling a precise engineering of microbial cells and communities.

scholarly journals DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity

2019 ◽  
Author(s):  
Matthew Carlucci ◽  
Algimantas Kriščiūnas ◽  
Haohan Li ◽  
Povilas Gibas ◽  
Karolis Koncevičius ◽  
...  
Keyword(s):  
Web Application ◽  
Statistical Significance ◽  
R Package ◽  
Biological Data ◽  
Supplementary Information ◽  
Statistical Knowledge ◽  
Health And Disease ◽  
Phase Amplitude ◽  
Almost All ◽  
User Friendly

Abstract Motivation Biological rhythmicity is fundamental to almost all organisms on Earth and plays a key role in health and disease. Identification of oscillating signals could lead to novel biological insights, yet its investigation is impeded by the extensive computational and statistical knowledge required to perform such analysis. Results To address this issue, we present DiscoRhythm (Discovering Rhythmicity), a user-friendly application for characterizing rhythmicity in temporal biological data. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). We optimized these algorithms for speed, improving their execution times up to 30-fold to enable rapid analysis of -omic-scale datasets in real-time. Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity. Availability and Implementation The DiscoRhythm R package is available on Bioconductor (https://bioconductor.org/packages/DiscoRhythm), with source code available on GitHub (https://github.com/matthewcarlucci/DiscoRhythm) under a GPL-3 license. The web application is securely deployed over HTTPS (https://disco.camh.ca) and is freely available for use worldwide. Local instances of the DiscoRhythm web application can be created using the R package or by deploying the publicly available Docker container (https://hub.docker.com/r/mcarlucci/discorhythm). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining

2020 ◽  
Vol 61 (5) ◽  
pp. 639-647
Author(s):  
Yan Du ◽  
Yoshihiro Hase ◽  
Katsuya Satoh ◽  
Naoya Shikazono
Keyword(s):  
Gamma Rays ◽  
Wild Type ◽  
End Joining ◽  
Complex Type ◽  
Single Base ◽  
In The Wild ◽  
Non Homologous End Joining ◽  
Dna Ends ◽  
Wild Type Control

Abstract To investigate the involvement of the non-homologous end joining (NHEJ) pathway in plant mutagenesis by ionizing radiation, we conducted a genome-wide characterization of the mutations induced by gamma rays in NHEJ-deficient Arabidopsis mutants (AtKu70−/− and AtLig4−/−). Although both mutants were more sensitive to gamma rays than the wild-type control, the AtKu70−/− mutant was slightly more sensitive than the AtLig4−/− mutant. Single-base substitutions (SBSs) were the predominant mutations in the wild-type control, whereas deletions (≥2 bp) and complex-type mutations [i.e. more than two SBSs or short insertion and deletions (InDels) separated by fewer than 10 bp] were frequently induced in the mutants. Single-base deletions were the most frequent deletions in the wild-type control, whereas the most common deletions in the mutants were 11–30 bp. The apparent microhomology at the rejoined sites of deletions peaked at 2 bp in the wild-type control, but was 3–4 bp in the mutants. This suggests the involvement of alternative end joining and single-strand annealing pathways involving increased microhomology for rejoining DNA ends. Complex-type mutations comprising short InDels were frequently detected in the mutants, but not in the wild-type control. Accordingly, NHEJ is more precise than the backup pathways, and is the main pathway for rejoining the broken DNA ends induced by ionizing radiation in plants.

Physiological genomic analysis of the brain renin-angiotensin system

2003 ◽  
Vol 285 (3) ◽  
pp. R498-R511 ◽  
Author(s):  
Robin L. Davisson
Keyword(s):  
Genomic Analysis ◽  
Renin Angiotensin System ◽  
Molecular Tools ◽  
American Physiological Society ◽  
Angiotensin System ◽  
Integrative Physiology ◽  
Renin Angiotensin ◽  
Electrolyte Homeostasis ◽  
Health And Disease ◽  
The Brain

The brain renin-angiotensin system (RAS) has long been considered pivotal in cardiovascular regulation and important in the pathogenesis of hypertension and heart failure. However, despite more than 30 years of study, the brain RAS continues to defy explanation. Our lack of understanding of how the brain RAS is organized at the cellular and regional levels has made it difficult to resolve long-sought questions of how ANG II is produced in the brain and the precise mechanisms by which it exerts its actions. A major reason for this is the difficulty in experimentally dissecting the brain RAS at the regional, cellular, and whole organism levels. Recently, we and others developed a series of molecular tools for selective manipulation of the murine brain RAS, in parallel with technologies for integrative analysis of cardiovascular and volume homeostasis in the conscious mouse. This review, based in part on a lecture given in conjunction with the American Physiological Society Young Investigator Award in Regulatory and Integrative Physiology (Water and Electrolyte Homeostasis Section), outlines the physiological genomics strategy that we have taken in an effort to unravel some of the complexities of this system. It also summarizes the principles, progress, and prospects for a better understanding of the brain RAS in health and disease.

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