Abstracts
March 1st, 2022
session1 - 21:00~ (JST/UTC+9)
Microbial glycococonjugate catabolism and synthesis
MicroGlycoDB and the significance of integrating glycan data from microbial species
Kiyoko F. Aoki-Kinoshita
Abstract
We have been developing a curated database of microbial glycoconjugates and catabolism, based on data provided by collaborators. Currently, this database consists of glycan-related pathways in Bifidobacterium bifidum, Bifidobacterium longum, Campylobacter jejuni, Cryptococcus neoformans, Mycobacterium abscessus, and Mycobacterium tuberculosis. Both glycans and glycan-related genes from all of these species are available. In particular, visualizations of these pathways in Campylobacter jejuni and Mycobacterium species allow users to investigate the relationship between the glycans and pathways within the microbial body in a diagram. All of the data in MicroGlycoDB is managed using Semantic Web technologies, which will allow easier integration with existing resources such as GlyCosmos. Future work will entail the development of a repository to allow users to upload their microbial glycan data in a consistent format to be visualized in MicroGlycoDB.
Structure-function relationships of beta-mannosyltransferases from Candida pathogenic yeasts
Yann Guerardel
Abstract
The yeast Candida albicans belongs to the human commensal digestive and vaginal flora but immunocompromised patients may develop systemic infections by C. albicans that are characterized by high morbidity and mortality. Typical to yeasts, the C. albicans cell wall is a complex structure containing a network of β-1,3 and β-1,6 glucans, surrounded by a mannose-rich glycoconjugate outer layer mainly composed of PPM (phosphopeptidomannan; sometimes referred as ‘mannan’) and mannoproteins. The pioneering work of Shigeo Suzuki’s research group from Tohoku Pharmaceutical University established that C. albicans expresses β-1,2-oligomannosides (β-Mans) at the surface of its cell wall, in contrast to most non-pathogenic yeast species such as Saccharomyces cerevisiae. These β-Man are found in the most pathogenic Candida species and are considered as virulence factors. Indeed, they were shown to display stronger antigenicity than α-linked oligomannosides during the humoral antibody response of mammals and fungal adherence to epithelial cells. Moreover, the role of β-Mans as adhesins for C. albicans has been established in a number of in vitro and in vivo model systems. During this presentation, I will recapitulate on-going efforts to characterize both structure and functions of enzymes responsible for the biosynthesis of β-1,2-oligomannosides in C. albicans that started in 2008 with the identification of a family of nine genes, named CaBMT1-9, that encode for putative β-1,2-mannosyltransferases (Bmts). The aim of our studies is to characterize CaBmts activities in order to better understand the biosynthetic pathways of β-Mans and the catalytic mechanism of each enzyme, with the longer term objective to guide the design of putative inhibitors. In particular, the availability of well-defined enzymes will permit us to assay the inhibitory activities of a library of synthetic carbohydrates toward individual steps of β-mannosylated oligosaccharides biosynthesis. Here I will focus on the analysis of CaBmt1, CaBmt3 and CaBmt4 that were shown to sequentially prime, elongate and polymerize β-1,2-oligomannosides on α-1,2-oligomannosides. Indeed, using naturally derived and synthetic oligomannosides, we have identified the precise acceptor substrates and characterized the enzymatic parameters of individual enzymes. Then, combining small angle X-ray diffraction (SAXS), in silico molecular modelization and site-directed mutagenesis of recombinant proteins, we propose a structural and catalytic model of CaBmts.
Extracellular polysaccharides and fungal pathogenesis
Tamara Doering
Abstract
Cryptococcus neoformans is an opportunistic yeast that is responsible for almost 200,000 deaths worldwide each year, mainly in immunocompromised individuals. Like other yeasts, this eukaryotic pathogen is surrounded by a cell wall, which is mainly composed of polysaccharides. In addition, it displays an elaborate polysaccharide capsule that is required for its virulence.
After a brief introduction to this microbe and its glycans, this talk will present two short stories about proteins with key roles in the biosynthesis of the cell wall and capsule, respectively. The first part of the presentation will discuss results of a genetic screen we designed to identify cryptococcal genes that influence interactions of the pathogen with cells of the infected mammalian host, specifically engulfment by phagocytes. Interestingly, one hit from this screen encoded a protein S-acyltransferase; absence of this gene caused dramatic defects in cryptococcal morphology, cell wall integrity, and virulence. Palmitoylome profiling identified specific substrates of this protein, including enzymes required for cell wall synthesis, which explained the mutant phenotypes.
The second part of the presentation will review how we have combined computational and experimental approaches to understand the regulation of polysaccharide capsule synthesis. By mapping the transcriptional network that regulates this process, we identified a key set of transcription factors that are required for normal capsule production. We recently found that one of these proteins influences the formation of giant (Titan) cells which are important in cryptococcal pathogenesis. These stories illustrate the power and importance to human health of studies at the intersection of glycobiology and microbiology.
Biography
Tamara Doering (doeringlab.com) was an undergraduate at Johns Hopkins University, where she worked in the groups of Saul Roseman and Michael Edidin. After graduation, she spent a year in the Roseman lab before entering Johns Hopkins Medical School, where she earned MD and PhD degrees in 1991. Her thesis work, with Jerry Hart and Paul Englund, was on GPI anchor biosynthesis in African trypanosomes. She next did a fellowship with Randy Schekman at the University of California at Berkeley, studying ER to Golgi transport of GPI-anchored proteins in yeast, and was a visiting scientist with Arturo Casadevall at Albert Einstein College of Medicine. After two years on the faculty of Pharmacology at Cornell Medical College, she moved in 1999 to the Molecular Microbiology Department at Washington University Medical School, where she is currently the Alumni Endowed Professor of Molecular Microbiology.
Tamara’s early research experiences introduced her to two themes that her NIH-funded lab still pursues: the biology of pathogenic eukaryotic microbes and the pathways by which glycan structures are made. Motivated by the fascinating biology and severe impact of the pathogenic yeast Cryptococcus neoformans, her lab studies cryptococcal glycan synthesis, particularly the extensive polysaccharide capsule that is its major virulence factor. In recent years she has broadened her research to include cryptococcal gene regulation, genome variants that influence virulence, and interactions of this yeast with cells of the infected host.
Beyond research, Tamara is dedicated to the development of trainees, which motivates her teaching and mentoring activities, and to career development and professional equity for women in science and medicine. She is a fellow of the AAAS and ASM, and a member of the ASCI. She has received Burroughs Wellcome Fund Awards in Biomedical Sciences and in Molecular Pathogenic Mycology and a Mentor Award from Washington University Medical School.
Technologies and strategies for glycomics and glycoproteomics
Kazuhiro Aoki
Abstract
The modern revolution in molecular biology is being driven to a large extent by advances in methods for analysis and manipulation of DNA, RNA, and proteins, biomolecules whose syntheses are all driven through the copying and translation of templates. Glycosylation is one of the most common post-translational modifications of proteins and is not driven through a guiding template, but rather through the concerted action of a series of biosynthetic enzymes whose expression varies among different cell types and developmental stages in living cells. Complex carbohydrates, also known by the generic term “glycans,” serve key functions as receptors and modulators, and both glycoproteins and glycolipids have been shown to contribute to a variety of intra- and intercellular events that influence multiple biological functions and events. Protein glycosylation is essential for protein folding, stability, and degradation. Importantly, a single glycoprotein molecule could carry several glycosylation sites with different glycan chains that can be altered in multiple human diseases, leading to a considerable number of multiple glycoforms with subtle differences in their properties. Thus, altered biosynthesis or degradation of glycoconjugates can lead to human diseases related to inflammation, cancer, neural injury, cardiovascular disease, metabolic disorders, and other significant human pathologies. Our laboratory developed sensitive, robust and quantitative glycomic methods to analyze complex glycans in a broad range of biological materials. We applied our glycomic methods to dissect the biochemical significance of human disorders and microbial interactions. Here, we demonstrate our recent study on dissecting glycosylation pattern on SARS-CoV2 and ACE2 expressed on HEK293 cells in order to see how glycosylation impacts the interaction between the spike protein and ACE2. Moreover, we discuss the structure of mucin glycosylation that can alter in response to mucosal infection and inflammation and how mucin glycans play roles against pathogen invasion.
Bacterial glycosylation, it's complicated
Christine Szymanski
Abstract
Each microbe has the ability to produce a wide variety of sugar structures that includes some combination of glycolipids, glycoproteins, exopolysaccharides and oligosaccharides. For example, bacteria may synthesize lipooligosaccharides or lipopolysaccharides, teichoic and lipoteichoic acids, N- and O-linked glycoproteins or their related S-layers, capsular polysaccharides, exopolysaccharides, poly-N-acetylglycosamine polymers, peptidoglycans, osmoregulated periplasmic glucans, trehalose or glycogen, just to name a few of the more broadly distributed sugar structures that have been studied. The composition of most of these glycans are typically dissimilar from those described in eukaryotes, both in the seemingly endless repertoire of sugars that microbes are capable of synthesizing and in the unique modifications that are attached to these carbohydrate residues. Furthermore, strain to strain differences in the carbohydrate building blocks used to create these glycoconjugates are the norm, and many strains possess additional mechanisms for turning on and off certain monosaccharide additions and/or modifications exponentially contributing to the structural heterogeneity observed by a single isolate and preventing any structural generalization at the species level. Also, in the past, a greater proportion of research effort was directed toward characterizing pathogens rather than commensals, as well as focusing on microbes that were simple to grow in large quantities and straightforward to genetically manipulate. These studies have revealed the complexity that exists among individual strains and have formed a foundation to now better understand how other microbes, hosts and environments further transform the glycan composition of a single isolate. These studies also motivate researchers to further explore microbial glycan diversity particularly as more sensitive analytical tools are developed to examine microbial populations in situ rather than in large scale from an enriched nutrient flask. This talk will emphasize many of these points using the common foodborne pathogen, Campylobacter jejuni, as the model microbe.
Biography
Christine Szymanski first began working with intestinal pathogens during her PhD in the Department of Medical Microbiology at the University of Alberta in Edmonton, Canada. She then joined the Enteric Diseases Program at the US Naval Medical Research Center in Silver Spring, Maryland for her postdoctoral studies prior to starting her own independent career first at the National Research Council in Ottawa, Canada and then back at the University of Alberta. Christine joined the Complex Carbohydrate Research Center at the University of Georgia in 2016.
Szymanski is a microbial glycobiologist that uses multidisciplinary techniques and relevant model systems to: 1) characterize bacterial glycoconjugate pathways, 2) exploit bacteriophage recognition proteins that bind these structures, and 3) understand the protective benefits of host milk oligosaccharides to develop novel therapeutics and vaccines for the prevention of diarrheal diseases and post-infectious neuropathies such as Guillain-Barré Syndrome. These studies have also expanded our knowledge of carbohydrate metabolism by the gut microbiota and the transfer of antibiotic resistance between bacteria.
March 2nd, 2022
session2 - 9:00~ (JST/UTC+9)
Microbial glycococonjugate catabolism and synthesis (Japanese and English Session)
Enzymes and proteins in carbohydrate metabolism of bifidobacteria: a structural view
Shinya Fushinobu 伏信 進矢
Abstract
Bifidobacteria have attracted significant attention as they provide health-promoting effects in the human gut microbiota. In this talk, I will introduce the current overview of the three-dimensional structures of enzymes and proteins involved in the uptake, degradation, and metabolism of various carbohydrates. Because some bifidobacterial species have been established symbiotic relationships with humans, structural studies of their carbohydrate-utilizing systems have revealed an interesting history of molecular coevolution with their hosts. As predominant colonizers in the infants’ gut, some bifidobacterial species have a series of transporters and enzymes peculiar to human milk oligosaccharides. Interestingly, Bifidobacterium bifidum and Bifidobacterium longum have completely different types of lacto-N-biosidases that cleave off a key disaccharide component in the catabolic system. The structural features of these lacto-N-biosidases suggest that they arose from different protein origins. Crystal structures of enzymes involved in the degradation of mucin glycoproteins provided a structural basis for the utilization of the mucus layer component as a sustainable nutrient supply. Energy-harvesting systems of bifidobacterial species from plant dietary oligosaccharides have been also studied in detail. The degradation system of β-arabinooligosaccharides, which are present in plant cell wall components called hydroxyproline-rich glycoproteins, was also found from B. longum. Structural analyses of these proteins and enzymes were also performed. Especially, β-L-arabinofuranosidase HypBA1 of glycoside hydrolase (GH) family 127 possesses the cysteine nucleophile as the first example of more than 160 GH families, and its mechanistic detail was revealed.
Biography
I am a Professor at the Laboratory of Enzymology in the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo located in Tokyo, Japan. Raised in Kure, Hiroshima, Japan. I obtained a Ph.D. degree in the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo in 1999. My research interests concern the structure and function of enzymes, mainly those of Carbohydrate-Active enZymes.
The website of our laboratory is here. http://enzyme13.bt.a.u-tokyo.ac.jp/index-e.html
Please follow my Twitter account: @sugargroove
Practical Production of Oligosaccharides Employing Phosphorylases
Motomitsu Kitaoka 北岡 本光
Abstract
Phosphorylase is a class of the enzymes catalyzing reversible phosphorolysis of glycoside to form sugar 1-phosphate. All of the phosphorylases reported to date catalyze an exowise phosphorolysis of glycosides with strict substrate specificity. Various oligosaccharides have been prepared from sugar 1-phosphates and acceptor molecules based on the reversibility and specificity of each phosphorylase. While phosphorylases are considered to be useful catalysts in the production of oligosaccharides, the relatively small number of known phosphorylases limits their application. Therefore, it would be valuable to find phosphorylases with novel substrate specificity. Each phosphorylase is categorized in one of the following families; glycosyltransferase (GT)4, GT35, glycoside hydrolase (GH)13, GH65, GH94, GH112, GH130, GH149, and GH161. The majority of phosphorylases phosphorolyze α- or β-glucosides to generate α- or β-Glc1P with anomeric retention or inversion. The GH112 and GH130 comprise phosphorlyases that act on β-galactosides to generate α-Gal1P and β-mannosides to generate α-Man1P, respectively.Combined actions of two phosphorylases often make it possible to produce particular oligosaccharides from cheap material. For instance, we produced 200 g/L of lacto-N-biose I (Galβ1,3GlcNAc) from sucrose and GlcNAc in one pot using the four enzymes including sucrose phosphorylase and 1,3-β-galactosyl-HexNAc phosphorylase. We have also developed a one-pot enzymatic glycosylation method from a free monosaccharide by using combined actions of an anomeric kinase and a phosphorylase with the ATP-regeneration system composed of pyruvate oxidase and acetate kinase by consuming pyruvic acid. This method is applicable for the syntheses of various oligosaccharides if the combination of anomeric kinase and phosphorylase is available. We prepared various β-galactosides and β-mannosides from galactose (with galactokinase) and mannose (with N-acetylhexosamine 1-kinase), respectively, using corresponding phosphorylases, with the productivity of around 100 g/L.
Biography
Graduated from Faculty of Engineering, The University of Tokyo in 1985, and after working for a private company, he earned his Ph. D. degree in 1993. From 1995 to 1998, he studied the reaction mechanism of dextran synthase as a postdoctoral fellow at Iowa State University. From 1998 to 2019, he was engaged in research focusing on the development of practical production technology for oligosaccharides using enzymes at the Food Research Institute, National Agriculture and Food Research Organization. He is now a professor at Niigata University since 2019.
Structures and functions of cell wall polysaccharides in various yeast species
Kaoru Takegawa 竹川 薫
Abstract
Glycosylation is a major covalent modification that modulates the structure and function of secretory and membrane proteins in eukaryotes. Yeast and most higher eukaryotes utilize an evolutionarily conserved oligosaccharide biosynthetic pathway. However, the oligosaccharide structures of yeasts, differ significantly from those of mammalian cells and humans, which has compromised their therapeutic utility. The difference between yeast and mammalian glycan structures of glycoproteins is a major problem for using yeasts as production hosts. Processing sugar transferases in the Golgi lead to the formation of core-sized structures (Hex<15GlcNAc2) as well as cores with an extended poly-1,6-Man `backbone' that is derivatized with various carbohydrate side chains in a species-specific manner (Hex50-200GlnNAc2). Yeasts vary greatly in the linkage and composition of their mannan side chains; some are as short as a single Gal residue, while others are complex polymannose side-chains containing phosphate and sugar residues other than Man.
The glycoproteins of Schizosaccharomyces pombe contain a large amount of galactose in addition to mannose, indicating that S. pombe is equipped with mechanisms for the galactosylation of glycoprotein like animal cells. Oligosaccharide structures of fission yeasts are constructed by continuous reactions of glycosyltransferases including mannosyl- and galactosyltransferases. S. pombe has 11 galactosyltransferase-related genes: seven belonging to glycosyltransferase (GT) family 34, three belonging GT family 8, and one belonging GT family 31. Using a combination of strains individually expressing and co-expressing galactosyltransferases, we are now in a position to genetically tailor the galactosylation of both N- and O-glycans in S. pombe. We will discuss current understanding of the biosynthetic pathway and physiological role of galactose-containing oligosaccharides in fission yeast.
Biography
I graduated from Kyoto University in 1986 (MSC), and obtained his Ph.D. degree in biochemistry (Faculty of Agriculture) from Kyoto University in 1990. I began my studies on the biological roles of the microbial endoglycosidase in Kyoto University and Kagawa University. I joined Dr. Scott Emr's laboratory of University of California, San Diego (1991-1993), where I studied the phosphatidylinositol 3-kinase encoded by yeast VPS34 gene essential for vacuolar protein sorting.
2008 to present: Professor at the Department of Bioscience and Biotechnology, Kyushu University. My current interests are structure and biosynthesis of cell wall polysaccharides from fungal cells.
Enzymes involved in mucin O-glycan degradation by Bifidobacterium bifidum
Takane Katayama 片山 高嶺
Abstract
Mucolytic bacteria are considered to play pivotal roles in modulating gut microbiota-host symbiosis and dysbiosis through their ability to degrade O-glycans. However, how, and to what extent, bacterial decomposition and fermentation of O-glycans affect homeostasis of gut ecosystem remain elusive. To elucidate the molecular basis underlying O-glycan-mediated physiology and pathology in the gut, we need to precisely understand both in vitro and in vivo function of each of O-glycan degrading enzymes of bacteria. In this talk, I will focus on Bifidobacterium bifidum, which is known to be a mucin O-glycan degrader and colonizes a wide range of mammalian guts. B. bifidum commonly possesses 10 extracellular enzymes responsible for hydrolyzing all glycosidic linkages found in mucin O-glycan, except α-linked GalNAc in blood group A substance, thereby releasing mono- and di-saccharides from O-glycan chains. I will talk about structure-function relationship underpinning unique substrate specificities of these enzymes and then show how these enzyme activities affect microbiota formation through cross-feeding to other gut microbes.
D-arabinan degradative enzymes of Microbacterium arabinogalactanolyticum for the assimilation of mycobacterial lipoarabinomannan.
Kiyotaka Fujita 藤田 清貴
Abstract
D-arabinofuranose (Araf) exists in the D-arabinan parts of the lipoarabinomannan (LAM) and arabinogalactan (AG) in the cell wall fraction of Mycobacteria. The D-arabinan structure is commonly constituted by α-1,5-D-Araf backbone with some α-1,3-D-Araf branching, and is terminated by β-1,2-Araf structure. Endo-D-arabinase is a D-arabinan degrading enzyme with endo-mode of action. The enzyme has been found in Microbacterium arabinogalactanolyticum, Cellulomonas sp. and Mycobacterium smegmatis, whereas the gene information has never been reported. Here, we would like to report the cloning and characterization of novel endo-D-arabinases (Endo-αDAbn1 and Endo-αDAbn2) from Mi. arabinogalactanolyticum JCM9171.
Endo-αDAbn1 is a novel glycoside hydrolase which has no similarities with any known CAZy GH families. The enzyme comprises 511 aa including a N-terminal signal peptide, a catalytic domain, and a C-terminal carbohydrate-binding domain. Endo-αDAbn2 (27% identity with Endo-αDAbn1) is located in same gene cluster. Endo-αDAbn2 comprises 369 aa including a N-terminal signal peptide and a catalytic domain. The recombinant enzymes degraded LAMs from My. smegmatis and My. tuberculosis, and released arabinooligosaccharides (DPs 1 - >20), whereas the degradation profiles were different in each enzyme. The enzymes also degraded AG from My. smegmatis. The substrate specificities were examined by using synthetic oligo-D-arabinofuranosides. We also characterized intracellular degradative enzymes exo-α-D-arabinofuranosidase (Exo-αDAbf) and exo-β-D-arabinofuranosidase (Exo-βDAbf).
Investigate carbohydrate metabolism in various environments using the distribution of glycan-related genes obtained from metagenomes
Hayato Takihara 瀧原 速仁
Abstract
With the development of high-throughput DNA sequencing technology, it has been increasing in amount of sequence and decreasing in experimental cost year by year. However, development of annotation of gene functions into nucleotide sequences and subsequent steps has not been so remarkable. Since the accuracy of annotating gene functions to nucleotide sequences is greatly affected by read length, chimera sequences, and sequence errors, the accuracy of short read sequences is reduced. As of January 2022, there are 2.37 million files of environmental metagenomes registered in NCBI SRA, of which 2.13 million files have been sequenced by Illumina’s sequencers. The read length obtained from the sequencers is 100-250 bp. The accuracy of gene function annotation for read sequences shorter than 700 bp is generally 55-80% (Rho et. al. 2010). It is insufficient to predict functions of environmental microorganisms using sequences obtained from environmental samples.
We have been organized by a gene database classified by the function of glycan-related genes and drug resistance genes, and collected functional distributions of genes in metagenomes of various environments such as oceans and soils using the information. We are working on developing a scheme to characterize and quantify environmental metagenomes and to compare them between the same or different environments. Glycan-related genes play roles of formation of glycoconjugate such as glycoprotein, and acquisition of ATP from carbohydrates. Investigating glycan-related genes in environmental microbiomes is useful for identifying the types of glycans utilized by microorganisms and polysaccharides they produce.
With our method, tens of millions of reads from about 200 metagenome data were annotated as glycan-related genes. The percentage of glycan-related genes was high in the human-associated environment, suggesting that these environments would utilize glycan metabolism better than other environments. Among the identified glycan-related genes, many glycoside hydrolase and glycosyltransferase were identified. There were two groups (1) identified in various environments mainly involved in monosaccharide metabolism, and (2) identified in specific environments involved in polysaccharide degradation. It was suggested that microorganisms would possess processes to obtain energy from carbohydrates in each environment and their functions would be adapted to the carbohydrates in the environments.
This method is expected to facilitate the evaluation of the potential of microbial carbohydrate metabolism in environments. We will evaluate the effect of carbohydrate metabolism on the host by investigating glycan-related genes in the human gut metagenomes in the future.
(1) Rho et. al. Nucleic Acids Res. 2010. 38:e191
session3 - 21:00~ (JST/UTC+9)
Microbial glycococonjugate catabolism and synthesis
Mycobacterial glycopeptidolipids : biosynthesis and biological functions
Louis-David LeClercq
Abstract
Mycobacterium abscessus (Mabs) is a recently discovered, fast-growing and non-tuberculous mycobacteria (NTMs) with an upward sloping incidence. Mabs can be observed either as a highly virulent rough form, or as a smooth form producing a lot of glycopeptidolipids (GPLs). Those cell-wall compounds are built around a peptide core esterified by a C24-C33 lipid at N-term, and an alaninol at C-term. Hydroxy groups are glycosylated by 6-dTal on a threonine and by one to two Rha on the alaninol, leading to GPL-2a and GPL-3. Recently, we showed that β-methoxy group, added on the lipid by fmt gene product, increase cell-wall hydrophobicity and ability to invade macrophage. Here, we focus on glycosylation by 3 potential glycosyltransferases gtf1, gtf2 and gtf3 and their linked to observed phenotypes. Finally, modification of the 6-dTal by selected acetyltransferases helped to consolidate the biosynthesis scheme.
Biography
https://www.linkedin.com/in/louis-david-leclercq-650581221
Mycobacterial arabinogalactan and glycosidases
Christophe Mariller
Abstract
The cell envelope of mycobacteria is remarkably complex and constitutes an impermeable barrier to therapeutic molecules as well as to the host's immune attack. It has the particularity of having characteristics that mix those of Gram + and Gram - bacteria (mycomembrane). The core of this envelope is the covalent mycolylarabinogalactan-peptidoglycan (mAGP) complex composed of peptidoglycan, arabinogalactan and mycolic acids from the inside to the outside. In this context, arabinogalactan constitutes the physical link between the peptidoglycan shell and the waxy layer of mycolic acids. It is a particular polysaccharide with a branched structure based on a galactan chain to which up to three arabinan chains are attached. The latter are esterified by mycolic acids at their non-reducing end. It is now recognized that the length of the galactan chain plays a complex role affecting mycobacteria growth, morphology and sensitivity to antibiotics. In this context, the identification of glycosidases able to modulate the size of the galactan chain is of great importance. We present here the first specific glycosidase of the galactan chain of mycobacteria, GlfH1. It is a secreted exogalactofuranosidase which has the particularity to be able to cleave alternatively the ß1-5 and ß1-6 bonds of the galactan chain. Moreover, its expression impacts the ability of the mycobacteria to multiply in an infection model.
Biography
https://www.researchgate.net/profile/Christophe-Mariller
March 3rd, 2022
session4 - 9:00~ (JST/UTC+9)
Glycosmos Portal (Japanese and English Session)
GlyCosmos Portal
Masae Hosoda 細田正恵, Akihiro Fujita 藤田晶大, Tamiko Ono 小野多美子, Shinichiro Tsuchiya 土屋伸一郎, Issaku Yamada 山田一作
Abstract
The GlyCosmos Portal is officially recognized by the Japanese Society of Carbohydrate Research, integrating and linking data in the glycosciences and life science related fields. Repositories, databases, tools, etc. are available on this site. In this session, we will first give an overview of the GlyCosmos Portal. After that, we will introduce the international glycan structure repository GlyTouCan. In particular the registration method, accession numbers, relation to GlyCosmos Glycans, etc., and the GlyTouCan Partner system will be described.
Next, we will introduce the GlyCosmos Data Resources. Specifically, the methods for acquiring information on related glycan structures, glycoproteins, lectins, and pathways when a certain microorganism is selected as an organism species will be described.
Regarding glycan information related to diseases, we will describe how to obtain 1) glycan structures as substrates of a particular target gene/enzyme and its related diseases, 2) the related diseases from the protein perspective, the glycan structure modifying the protein, and the related pathways.
Finally, we will explain how to use various tools available on the GlyCosmos portal. After explaining the SNFG notation, which is the standard for representing glycan structures, SugarDrawer and GlycanBuilder2, which are tools for drawing, editing, and searching glycans, will be demonstrated in finding glycans found in particular microorganisms. In addition to the above methods, GlyCosmos can be used to search for glycan structures by various methods. As one of them, we will explain how to use the text search tool that easily converts between various text formats for glycans. In addition, a tool for acquiring an image of a glycan structure from the accession number of GlyTouCan will be explained. These tools can be used when searching data when the glycan structure notation differs between databases.
In this way, GlyCosmos contains various data such as genes, proteins, diseases, and pathways in addition to glycans. More detailed information can be found on the linked database site. Thus, GlyCosmos aims to serve as a window for various glycan-related data. We will continue to develop GlyCosmos with the aim of helping the development of glycoscience and to create a site that is easy for anyone to use.
session5 - 21:00~ (JST/UTC+9)
GlySpace Alliance
The GlyCosmos Glycoscience Portal
Kiyoko F. Aoki-Kinoshita
Abstract
GlyCosmos (https://glycosmos.org) is a Web portal for glycoscience data, accumulating and integrating glycan-related omics data from a variety of resources, storing them using Semantic Web technologies. Keyword search is available for all of the data resources including glycogenes, glycoproteins, lectins, pathways and diseases. The Repositories section includes the glycan repository GlyTouCan, glycomics raw data repository GlycoPOST, glycomics repository UniCarb-DR, and a newly developed glycoconjugate repository prototype GlyComb, due to be released in March. As a member of the GlySpace Alliance, all the data is freely shared under a CC-BY-4.0 license. The latest additions and functionality will be introduced.
GlyGen
Rene Ranzinger
Abstract
Advancing our understanding of the roles that glycosylation plays in development and disease is frequently hindered by the diversity of the data that must be integrated to gain insight into these complex phenomena. GlyGen is a maturing initiative, supported by the NIH Common Fund, with the goal of democratizing glycoscience research by developing and implementing a comprehensive data repository that integrates diverse types of data, including glycan structures, glycan biosynthesis enzymes, glycoproteins, along with genomic and proteomic knowledge. To achieve the highest possible integration and impact, GlyGen has established international collaborations with database providers from different domains (including but not limited to EBI, NCBI, PDB, GlyTouCan and UniCarbKB) and glycoscience researchers. Information from these resources and groups are standardized and cross-linked to allow queries across multiple domains. To facilitate easy access to this information, an intuitive, web based interface (https://glygen.org) has been developed to visually represent the data and the connections between datasets. In addition to the browser-based interface we are also developing RESTful webservice-based APIs and a SPARQL endpoint, allowing programmatic access to integrated datasets.
For each glycan and glycoprotein in the dataset, GlyGen provides a details page that integrates all available information. Individual details pages are interlinked with each other allowing easy data exploration across multiple domains. For example, users can browse from the webpage of a glycosylated protein to the glycan structures that have been described to be attached to this protein, and, from there, to other proteins that carry the same glycan. All information accessed through GlyGen is linked back to original sources, allowing users to browse through information pages in other resources. Our goal is to provide scientists with an easy way to access the complex information underlying state-of-the-art knowledge that describes the biology of glycans and glycoproteins. In order to facilitate easy entry into GlyGen datasets independent of previous knowledge of glycoscience, we have developed a new graphical interface that allows users to access glycan and glycosylation data. All available data in GlyGen is represented as a graph consisting of nodes (glycans, proteins, disease, organism etc,) and edges that connect these nodes (glycans is attached to proteins, glycans have motifs etc.). By interacting with the nodes users can specify search criteria to filter the available data based on their area of interest. The interface allows building very complex queries which cannot be answered by traditional databases and their search interfaces. Once the query is built and submitted, users can explore the identified proteins, glycans, or glycosylation sites in detail. This new entry pathway will facilitate the generation of hypotheses regarding functional roles of glycans, glycosyation, and glycoproteins.
To schedule a demo of GlyGen or add your data to GlyGen contact Michael Tiemeyer (mtiemeyer@ccrc.uga.edu) or Raja Mazumder (mazumder@gwu.edu).
Improved consistency in inter-related glyco-data
Frederique Lisacek
Abstract
Glycomics and glycoproteomics data accumulate in publications, and if not for glycoinformatics, glycome data collection, browsing and comparison would not be possible. Often enough, glycan structures are partially resolved and glycoinformatics tools have to be designed to cope with ambiguity and uncertainty. Our latest efforts to set rules that allow loose yet meaningful searches in glyco-databases will be introduced and illustrated.