Article
Biochemistry & Molecular Biology
Yogita Sharma, Shimona Ahlawat, Alka Ashish, Alka Rao
Summary: This study describes the shape-function relationship of SvGT (S/O-HexNActransferase) in the glycosylation process of bacteriocin SvC (ORF AQF52_3099) in Streptomyces venezuelae ATCC 15439. Experimental data confirmed that SvGT protein adopts an elongated dimeric shape in solution. The activation of SvGT requires the availability of Mg2+ ions, as confirmed by enzyme assays. SAXS analysis revealed the structural changes induced by Mg2+ ions and the role of conserved residues in the catalytic motif of SvGT.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Yogita Sharma, Shimona Ahlawat, Alka Rao
Summary: This study provides experimental evidence for S-glycosylation in Actinobacteria and demonstrates the application of its S/O-HexNAc-transferase in glycocin engineering, generating new neoglycocins against Listeria monocytogenes.
Article
Chemistry, Multidisciplinary
Yongliang Wei, Benjamin Ben-zvi, Tianning Diao
Summary: C-aryl glycosyl compounds offer improved in vivo stability compared to O- and N-glycoside analogues, making them attractive candidates for drug development and chemical biology studies. A new cross-coupling method has been developed for the preparation of C-aryl and heteroaryl glycosides, including nucleosides and 2-deoxysugars, from easily accessible glycosyl esters and bromoarenes, demonstrating the potential of this method in medicinal chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Plant Sciences
Richard Strasser, Georg Seifert, Monika S. Doblin, Kim L. Johnson, Colin Ruprecht, Fabian Pfrengle, Antony Bacic, Jose M. Estevez
Summary: Glycosylation is a crucial modification process that can alter the biological function of proteins and lipids, affecting the development and physiology of an organism. While challenges remain in understanding plant glycosylation, high throughput approaches may help to address these gaps, revolutionizing the identification and characterization of unknown plant glycosyltransferases and hydrolases.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Physical
David Teze, Joan Coines, Folmer Fredslund, Kshatresh D. Dubey, Gonzalo N. Bidart, Paul D. Adams, John E. Dueber, Birte Svensson, Carme Rovira, Ditte H. Welner
Summary: The study found that UGT1 from Polygonum tinctorium can catalyze N-, O-, or S-glycosylation with similar rates, and elucidated the molecular basis of N-, O-, and S-specificities using experimental mutagenesis and simulations. It also showed that the active site can be engineered to increase or favor one of the three glycosylation activities over another, leading to the design of more active and specific enzyme variants for glycoside production.
Article
Multidisciplinary Sciences
Eugenia Wulff-Fuentes, Jeffrey Boakye, Kaeley Kroenke, Rex R. Berendt, Carla Martinez-Morant, Michaela Pereckas, John A. Hanover, Stephanie Olivier-Van Stichelen
Summary: The study investigates the role of O-GlcNAcylation in regulating the solubility and aggregation of OTX2 protein, potentially preventing OTX2 aggregation through its interaction with CCT5 protein. Additionally, O-GlcNAc-depleted OTX2 is detrimental to cancer cells.
Article
Biotechnology & Applied Microbiology
Silvia-Simona Grosu-Tudor, Iulia-Roxana Angelescu, Alexandru Brinzan, Medana Zamfir
Summary: S-layer proteins produced by lactobacilli isolated from Romanian artisan fermented products were characterized. The presence of S-layer proteins was confirmed by electron microscopy, and their removal caused a loss of bacterial resistance and self-aggregation ability. Liquid chromatography-mass spectrometry analysis identified the molecular masses and isoelectric points of the proteins. PCR amplification revealed the similarity between the genome of Lact. helveticus 34.9 and slpA gene.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Ji-Young Lee, Hyeon-Su Jin, Kyoung Su Kim, Je-Hyun Baek, Bong-Soo Kim, Dong-Woo Lee
Summary: Akkermansia muciniphila is a key player in regulating the human gut microbiota through mucin degradation. It mainly relies on the Embden-Meyerhof-Parnas pathway for energy production and short-chain fatty acid production through anaerobic fermentation under specific nutrient conditions. The bacterium has a diverse array of glycosyl hydrolases, peptidases, and sulfatases for breaking down O-glycosylated mucin, with specific mucin-degrading enzymes being highly abundant in mucin-supplemented media.
Article
Microbiology
Can Zhang, Meng Cai, Shanshan Chen, Fan Zhang, Tongshan Cui, Zhaolin Xue, Weizhen Wang, Borui Zhang, Xili Liu
Summary: In this study, a glycoproteomic analysis of Phytophthora sojae was conducted to identify N-glycosylated proteins, confirming the essential role of multiple N-glycosylation motifs in the growth of this oomycete. Through mutagenesis experiments, it was demonstrated that N-glycosylation of specific proteins is crucial for cyst germination and oospore production. These findings provide insights into the role of N-glycosylation in the development of oomycetes.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
John Kelly, Evgeny Vinogradov, Anna Robotham, Luc Tessier, Susan M. Logan, Ken F. Jarrell
Summary: This study reports the N- and O-glycosylation modifications in Methanoculleus marisnigri, a methanogen from the Order Methanomicrobiales. Mass spectrometry and NMR analysis revealed the presence of N- and O-glycans in the S-layer protein, but not in the archaellins. The findings provide insights into the glycosylation diversity in archaea.
Article
Microbiology
Benedicte Colnet, Christian M. K. Sieber, Fanny Perraudeau, Marion Leclerc
Summary: This study aimed to predict the growth capacity of Bacteroidetes-type strains on fibers using genomic sequences. The prediction performance of the in silico pipeline FiberGrowth varied for different fibers, showing different true positive rates and false positive rates based on available data.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Elena Jimenez-Ortega, Egle Narmontaite, Beatriz Gonzalez-Perez, Francisco J. Plou, Maria Fernandez-Lobato, Julia Sanz-Aparicio
Summary: This study presents the structure and function of Rhodotorula dairenensis β-fructofuranosidase, an enzyme with broad substrate specificity and unique structural features. The research also identifies key residues that play a crucial role in the enzyme's activity and generates variants with redesigned transfructosylating specificity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Food Science & Technology
Jose M. Landete
Summary: The study aims to increase the concentration of O-DMA and 6-OH-O-DMA compounds in fermented beverages through the metabolism of lactic acid bacteria (LAB), in order to develop functional soy beverages enriched in O-DMA, 6-OH-O-DMA, daidzein and genistein.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Shiori Oka, Miyuki Watanabe, Emi Ito, Ami Takeyama, Takuro Matsuoka, Masatomo Takahashi, Yoshihiro Izumi, Norihito Arichi, Hiroaki Ohno, Sho Yamasaki, Shinsuke Inuki
Summary: Recently, it has been reported that various metabolites derived from host microbes can modulate the immune system, and may play a role in health and diseases. However, the connection between archaea, prokaryotic organisms, and the host is not well understood compared to other microorganisms like bacteria. This study focused on unique glycerolipids from symbiotic methanogenic archaea and their interaction with an innate immune receptor called Mincle. The findings suggest that archaeal lipids are recognized by Mincle and induce immune responses, highlighting their potential impact on host health and diseases.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Food Science & Technology
Burcu Ozturk, Mensure Elvan, Merve Ozer, Sebnem Tellioglu Harsa
Summary: This study evaluated the viability and bioaccessibility of Streptococcus thermophilus CCM4757 strain in dark and milk chocolates during storage and simulated in vitro gastrointestinal tract passage. The microencapsulated S. thermophilus showed good survivability in both types of chocolates during storage. Supplementation of S. thermophilus did not significantly affect the sensory attributes of the chocolates, demonstrating its potential as a probiotic carrier in chocolate matrices.
Article
Dentistry, Oral Surgery & Medicine
Fabian L. Kendlbacher, Susanne Bloch, Fiona F. Hager-Mair, Johanna Bacher, Bettina Janesch, Thomas Thurnheer, Oleh Andrukhov, Christina Schaeffer
Summary: This study compared the periodontitis-associated bacterium Tannerella forsythia with its closest phylogenetic relative Tannerella serpentiformis, which is considered health-associated. The results showed that the presence of T. serpentiformis in oral biofilms led to a decrease in total bacteria count, while T. forsythia promoted biofilm growth. However, when added together, T. serpentiformis mitigated the growth-promoting effect of T. forsythia. T. serpentiformis outcompeted T. forsythia in the biofilm and had a more even distribution throughout the biofilm. In invasion assays, T. serpentiformis was less effective in invading human gingival epithelial cells compared to T. forsythia. In addition, T. serpentiformis had a higher immunostimulatory potential in human gingival fibroblasts and macrophages. These findings suggest that T. serpentiformis has the potential to interfere with processes relevant to the development of periodontitis.
MOLECULAR ORAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Sergio Tomas-Martinez, Le Min Chen, Martin Pabst, David G. Weissbrodt, Mark C. M. van Loosdrecht, Yuemei Lin
Summary: Pseudaminic and legionaminic acid are types of nonulosonic acids (NulOs) found only in bacterial species. Limited progress has been made in studying these NulOs due to their complex synthesis and production. Recent research has discovered that Candidatus Accumulibacter produces analogues of Pse and Leg as part of its extracellular polymeric substances (EPS). By extracting EPS from Ca. Accumulibacter and using size-exclusion chromatography (SEC), it was found that high molecular weight polysaccharides contained NulOs at levels up to four times higher than the extracted EPS. Additionally, the extracted EPS and NulO-rich fractions were found to bind and neutralize histones, indicating their potential as a source for sepsis treatment drugs.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Christina Sophie Hausjell, Wolfgang Ernst, Clemens Gruenwald-Gruber, Elsa Arcalis, Reingard Grabherr
Summary: Due to its suitability in producing complex biopharmaceutical products, the baculovirus/insect cell expression system has become popular in the biotechnological industry. Extracellular vesicles (EVs), small particles used for intracellular communication, may play a significant role in virus-cell communication and infection spreading. This study isolated and characterized EVs from both uninfected and baculovirus infected Tnms42 insect cells and found significant changes in EV protein cargo upon infection, suggesting a major role of EVs as stress markers. The findings may contribute to improving biopharmaceutical production within the baculovirus/insect cell expression system through the development of new process monitoring and control tools.
Article
Biotechnology & Applied Microbiology
Sergio Tomas-Martinez, Erwin J. Zwolsman, Franck Merlier, Martin Pabst, Yuemei Lin, Mark C. M. van Loosdrecht, David G. Weissbrodt
Summary: Polyphosphate accumulating organisms (PAOs) play a crucial role in the removal of phosphate from wastewater. However, little is known about the dynamics of extracellular polymeric substances (EPS) in mixed cultures and their interaction with flanking microbes. Understanding EPS turnover can provide insights into their biosynthesis and degradation cycles.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Daphne Keulen, Erik van der Hagen, Geoffroy Geldhof, Olivier Le Bussy, Martin Pabst, Marcel Ottens
Summary: An optimal purification process for biopharmaceutical products is crucial for meeting safety regulations and obtaining economic benefits. By employing artificial neural networks (ANNs) during global optimization, the number of flowsheets for final local optimization can be reduced, leading to a shorter overall optimization time.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemical Research Methods
Roxana Disela, Olivier Le Bussy, Geoffroy Geldhof, Martin Pabst, Marcel Ottens
Summary: Mass-spectrometry-based proteomics is used to monitor purification processes and detect host cell proteins in the final drug substance. It provides unbiased identification of individual host cell proteins. Proteomics can provide qualitative and quantitative information on the host cell proteome before purification, enabling a more rational design of purification strategies. This study presents an extensive proteomic characterization of two commonly used E. coli host cell strains and integrates subunit information and post-translational modifications.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Allergy
Stephanie Dramburg, Christiane Hilger, Alexandra F. Santos, Leticia de las Vecillas, Rob C. Aalberse, Nathalie Acevedo, Lorenz Aglas, Friedrich Altmann, Karla L. Arruda, Riccardo Asero, Barbara Ballmer-Weber, Domingo Barber, Kirsten Beyer, Tilo Biedermann, Maria Beatrice Bilo, Simon Blank, Philipp P. Bosshard, Heimo Breiteneder, Helen A. Brough, Merima Bublin, Dianne Campbell, Luis Caraballo, Jean Christoph Caubet, Giorgio Celi, Martin D. Chapman, Maksymilian Chruszcz, Adnan Custovic, Rebecca Czolk, Janet Davies, Nikolaos Douladiris, Bernadette Eberlein, Motohiro Ebisawa, Anna Ehlers, Philippe Eigenmann, Gabriele Gadermaier, Mattia Giovannini, Francisca Gomez, Rebecca Grohman, Carole Guillet, Christine Hafner, Robert G. Hamilton, Michael Hauser, Thomas Hawranek, Hans Juergen Hoffmann, Thomas Holzhauser, Tomona Iizuka, Alain Jacquet, Thilo Jakob, Bente Janssen-Weets, Uta Jappe, Marek Jutel, Tanja Kalic, Sandip Kamath, Sabine Kespohl, Joerg Kleine-Tebbe, Edward Knol, Andre Knulst, Jon R. Konradsen, Peter Korosec, Annette Kuehn, Gideon Lack, Thuy-My Le, Andreas Lopata, Olga Luengo, Mika Maekelae, Alessandro Maria Marra, Clare Mills, Martine Morisset, Antonella Muraro, Anna Nowak-Wegrzyn, Roni Nugraha, Markus Ollert, Kati Palosuo, Elide Anna Pastorello, Sarita Ulhas Patil, Thomas Platts-Mills, Anna Pomes, Pascal Poncet, Ekaterina Potapova, Lars K. Poulsen, Christian Radauer, Suzana Radulovic, Monika Raulf, Pierre Rouge, Joaquin Sastre, Sakura Sato, Enrico Scala, Johannes M. Schmid, Peter Schmid-Grendelmeier, Denise Schrama, Helene Senechal, Claudia Traidl-Hoffmann, Marcela Valverde-Monge, Marianne van Hage, Ronald van Ree, Kitty Verhoeckx, Stefan Vieths, Magnus Wickman, Josefina Zakzuk, Paolo M. Matricardi, Karin Hoffmann-Sommergruber
Summary: Since the discovery of IgE as a mediator of allergic diseases, our knowledge about its immunological mechanisms has greatly increased. Innovations in bioscience and technology have facilitated the production of well-defined molecules for component-resolved diagnosis, allowing personalized management of allergic diseases. The Molecular Allergology User's Guide 2.0 provides updated information on allergen molecules, their clinical relevance, and diagnostic algorithms, serving as a valuable resource for clinicians and scientists.
PEDIATRIC ALLERGY AND IMMUNOLOGY
(2023)
Article
Engineering, Environmental
Francesc Corbera-Rubio, Michele Laureni, Nienke Koudijs, Simon Mueller, Theo van Alen, Frank Schoonenberg, Sebastian Luecker, Martin Pabst, Mark C. M. van Loosdrecht, Doris van Halem
Summary: Rapid sand filters (RSF) are commonly used for groundwater treatment, however, the processes controlling the removal of iron, ammonia, and manganese are not well understood. This study investigated two drinking water treatment plant configurations and found that the removal of ammonium and manganese only occurred after iron depletion. The microbial composition and media coating within each compartment were found to be homogeneous, indicating the effect of backwashing. However, the removal of contaminants was stratified within each compartment, with proteins catalyzing ammonia oxidation and nitrifying genera showing significant differences in abundances between top and bottom samples. These findings highlight the potential of metaproteomics in understanding metabolic adaptations and interactions in dynamic ecosystems.
Article
Chemistry, Multidisciplinary
Albert Godoy-Hernandez, Amer H. Asseri, Aiden J. Purugganan, Chimari Jiko, Carol de Ram, Holger Lill, Martin Pabst, Kaoru Mitsuoka, Christoph Gerle, Dirk Bald, Duncan G. G. McMillan
Summary: LMNG Auto-insertion Reintegration (LAiR) is a new method that allows for rapid reintegration of integral membrane proteins, displaying excellent functional recovery capabilities, and playing a significant role in the study of membrane proteins.
ACS CENTRAL SCIENCE
(2023)
Article
Ecology
Dimitry Y. Y. Sorokin, Tamara V. V. Tikhonova, Hanna Koch, Eveline M. M. van den Berg, Renske S. S. Hinderks, Martin Pabst, Natalia I. I. Dergousova, Anastasia Y. Y. Soloveva, Gijs J. J. Kuenen, Vladimir O. O. Popov, Mark C. M. van Loosdrecht, Sebastian Lucker
Summary: This study discovered a new copper-depleted dissimilatory nitrate-reducing organism called Trichlorobacter ammonificans. It can actively grow using acetate as the electron donor and carbon source, and nitrate as the electron acceptor, with hydrogen as an additional electron donor. The organism uses an octaheme cytochrome c protein called TaNiR to carry out the dissimilatory nitrate reduction. These findings highlight the importance of this organism in various anaerobic systems such as rice paddy soil and wastewater treatment facilities.
Article
Biotechnology & Applied Microbiology
Benjamin Kogelmann, Roman Palt, Daniel Maresch, Richard Strasser, Friedrich Altmann, Somanath Kallolimath, Lin Sun, Marc-Andre DAoust, Pierre-Olivier Lavoie, Pooja Saxena, Johannes S. S. Gach, Herta Steinkellner
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Christina Sophie Hausjell, Miriam Klausberger, Wolfgang Ernst, Reingard Grabherr
Summary: The baculovirus/insect cell expression system is a versatile production platform in the biopharmaceutical industry, capable of producing high-titer complex protein assemblies. It is considered a promising option for manufacturing vaccine candidates, such as virus-like particles (VLPs). However, the co-formation of budded baculovirus during VLP production presents challenges for downstream processing.
Article
Engineering, Environmental
Ali Elahinik, Linghang Li, Martin Pabst, Ben Abbas, Dimitrios Xevgenos, Mark C. M. van Loosdrecht, Mario Pronk
Summary: This study investigated the conversion of glucose and its impact on phosphate removal by aerobic granular sludge. The results demonstrated that glucose could be used as a suitable substrate for achieving phosphate removal and that a microbial community consisting of fermentative organisms and polyphosphate accumulating organisms (PAO) developed.
Article
Biochemical Research Methods
Martin Holub, Anthony Birnie, Aleksandre Japaridze, Jaco van der Torre, Maxime den Ridder, Carol de Ram, Martin Pabst, Cees Dekker
Summary: Chromosome structure and function were studied through various cell-based methods and in vitro single-molecule techniques. The researchers developed a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. By isolating chromosomes from bacterial cells and enzymatically digesting native proteins, they removed DNA-binding proteins and observed DNA compaction and motion. The study suggests the feasibility of a "genome-in-a-box" approach to study chromosome organization.
CELL REPORTS METHODS
(2022)
Article
Biochemical Research Methods
Pin-Rui Su, Li You, Cecile Beerens, Karel Bezstarosti, Jeroen Demmers, Martin Pabst, Roland Kanaar, Cheng-Chih Hsu, Miao-Ping Chien
Summary: Single-cell proteomics has the potential to decode tumor heterogeneity, but current methods lack the ability to link individual cell proteomes with phenotypes of interest. Therefore, we developed a microscopy-based technology called FUNpro that allows real-time screening, identification, and isolation of specific single cells, even if the phenotypes are dynamic or the cells of interest are rare. We applied FUNpro to analyze a small subpopulation of U2OS osteosarcoma cells with abnormal, prolonged DNA damage response after ionizing radiation (IR) and identified the PDS5A protein as a contributor to the abnormal DDR dynamics and cell survival after IR.
CELL REPORTS METHODS
(2022)