Article
Biochemistry & Molecular Biology
Dominik A. Machtens, Jonas M. Willerding, Susanne Eschenburg, Thomas F. Reubold
Summary: The Gram-negative bacterium Legionella pneumophila is an accidental human pathogen that causes Legionellosis. During infection, L. pneumophila injects more than 300 effector proteins into the host cell to modify the intracellular environment and create a stable compartment for proliferation. The effector protein SidI inhibits host translation by interacting with eEF1A and may have a toxic effect due to its glycosyltransferase domain.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Microbiology
Emily C. Hoedt, Francesca Bottacini, Nora Cash, Roger S. Bongers, Kees van Limpt, Kaouther Ben Amor, Jan Knol, John MacSharry, Douwe van Sinderen
Summary: Members of the genus Bifidobacterium are difficult to genetically manipulate due to their extensive and variable Restriction-Modification systems. A modified suicide vector, pFREM28, was developed to target specific genes in B. breve by removing known restriction sites, reducing the time, effort, and resources required for generating site-directed mutants. This approach could be applied to other (bifido)bacterial species as well.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Soroosh Pouyan, Milad Lagzian, Mohammad Hossein Sangtarash
Summary: This study characterized a new alpha-amylase from Bacillus cereus GL96 and used an in-silico approach to redesign the enzyme for improved thermal stability. The engineered enzyme showed higher stability and activity at elevated temperatures compared to the wild-type enzyme. Specifically, the D162K mutation resulted in the best performance, with increased optimum temperature and improved stability. This mutant enzyme holds promise for further investigation and industrial applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Chemistry, Organic
Houchao Xu, Jeroen S. Dickschat
Summary: In the past three decades, numerous terpene synthases have been characterized from various life kingdoms. The mechanisms of terpene synthases have been investigated through site-directed mutagenesis, providing valuable insights into their catalysis and resulting in mutants with improved yields.
SYNTHESIS-STUTTGART
(2022)
Article
Computer Science, Software Engineering
Madhavi Latha Yadav Bangaru, Ravi Kumar Medabalimi, Sobhan Babu, Nidhanapati K. Raghavendra
Summary: Silent mutations allowing for restriction site modification can aid in screening successful mutants during site-directed mutagenesis. However, introducing a new restriction site requires the analysis of degenerate sequences within mutant primers, which becomes increasingly laborious, time-consuming, and prone to errors as the number of degenerate codons increases. A software named 'REMP' was developed to instantly generate degenerate sequences with restriction sites that are 6-8 base pairs in length, allowing users to edit the list of restriction sites without the need for writing computer code or knowing a program language.
Article
Biochemistry & Molecular Biology
Krzysztof Michalski, Christian Hertig, Dariusz R. Mankowski, Jochen Kumlehn, Janusz Zimny, Anna M. Linkiewicz
Summary: Cas endonuclease-mediated genome editing offers a long-awaited molecular biological approach for modifying predefined genomic target sequences in living organisms. The implementation of this technology can be challenging for species like triticale, but pre-validated cas9/gRNA constructs provide a strong foundation for the targeted induction of heritable modifications in triticale genes. The study also demonstrates that in-del induction frequency in triticale can be increased by TREX2 nuclease activity, regardless of gRNA performance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Hai-Yan Zhou, Xiao-Nan Yi, Qi Chen, Jian-Bao Zhou, Shu-Fang Li, Xue Cai, De-Shui Chen, Xin-Ping Cheng, Mian Li, Hong-Yan Wang, Kai-Qian Chen, Zhi-Qiang Liu, Yu-Guo Zheng
Summary: In this study, a novel endoglucanase (CgEndo) from Colletotrichum graminicola was modified by site-directed mutagenesis to improve its catalytic efficiency. Two mutants, Y63S and N20D/S113T, showed significantly increased enzyme activities. The mutations improved the proximity between the enzyme and its substrate, leading to higher enzyme activities and catalysis efficiency. These findings lay an important foundation for further engineering of the endoglucanase and its practical application in efficient degradation of cellulosic biomass.
ENZYME AND MICROBIAL TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kemin Lv, Wenyu Shao, Marcelo Monteiro Pedroso, Jiayu Peng, Bin Wu, Jiahuang Li, Bingfang He, Gerhard Schenk
Summary: In this study, the processive endoglucanase EG5C-1 from Bacillus subtilis was used as the basis for enzyme engineering, resulting in the discovery of variants D70Q and S235W, as well as the double mutant D70Q/S235W, which showed significantly improved activity towards substrates CMC and Avicel. Kinetic measurements demonstrated that the double mutant had higher substrate affinity and catalytic efficiency.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Magdalena Klimek-Chodacka, Miron Gieniec, Rafal Baranski
Summary: The study demonstrates an efficient, recombinant DNA-free, multiplex gene-editing method using gRNA:Cas9 ribonucleoprotein (RNP) complexes delivered directly to plant protoplasts. By forming three RNPs in vitro and delivering them to protoplasts, various editing effects were achieved with high efficiency, showcasing the potential of this method.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Tingting Wang, Zhiming Jiang, Yiya Wang, Hao Wu, Yan Fang, Weiliang Dong, Bin Wu, Jiangfeng Ma, Min Jiang
Summary: Mutation of amino acids near the sucrose binding site of dextransucrase can affect the chain elongation process, making it possible to modulate dextran size.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nur Aqlili Riana Alias, Adelene Ai-Lian Song, Noorjahan Banu Alitheen, Raha Abdul Rahim, Siti Sarah Othman, Lionel Lian Aun In
Summary: The secretion efficiency of heterologous proteins in Lactococcus lactis has been improved through the use of a mutated heterologous signal peptide SPK1. Four out of eight tested SPK1 variants enhanced the secretion of a reporter nuclease, with the best mutant, SPKM19, showing an 88% increase in secretion efficiency. This study demonstrates the potential for developing more effective heterologous signal peptides in the lactococcal host.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Huiyong Jia, Ricardo Couto-Rodriguez, Sharon Johnson, Stephanie Medina, Brianna Novillo, Peter Huynh, Matt Kim, Cade Cooper, Meagan Michalik, Benjamin Siew, Elise Turesson, Julie A. Maupin-Furlow
Summary: This study reports two new methods for site-directed mutagenesis of plasmids, which overcome the current issues of low efficiency, complexity, and time consumption. Both methods have high efficiency and can generate and isolate the appropriate DNA products with site-directed mutations.
Article
Biochemistry & Molecular Biology
Sitian Gu, Xiaojun Dai, Jiang Jiang, Yuanfa Liu
Summary: In this study, three single-site mutations were introduced into OaCLH to improve its catalytic efficiency. The mutants W160R and V228C showed significantly increased enzyme affinity and catalytic activity against all substrates, while the D224 N mutant changed its preferred substrate. These findings provide structural basis information for the catalytic activity and substrate specificity of OaCLH.
PROCESS BIOCHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Yasuyuki Nakamura, Ririka Asama, Takuya Tabata, Kenta Morita, Tatsuo Maruyama, Akihiko Kondo, Jun Ishii
Summary: Researchers utilized a yeast-based biosensor to analyze signal activation of melatonin receptors, finding that most mutations significantly affected the function of these receptors. This system holds promise for revealing the functions of melatonin receptors.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Danielle Williams, Weronika Brzezinski, Heather Gordon, Vincenzo De Luca
Summary: The study explores the formation pathway of the most abundant monoterpenoid indole alkaloids in Catharanthus roseus roots. It reveals the structural differences between V19H and T3O and provides experimental evidence for the common ancestor hypothesis between V19H and T3O.
Article
Infectious Diseases
Sergio Villanueva-Saz, Jacobo Giner, Ana Pilar Tobajas, Maria Dolores Perez, Andres Manuel Gonzalez-Ramirez, Javier Macias-Leon, Ana Gonzalez, Maite Verde, Andres Yzuel, Ramon Hurtado-Guerrero, Julian Pardo, Llipsy Santiago, Jose Ramon Pano-Pardo, Hector Ruiz, Delia Maria Lacasta, Lourdes Sanchez, Diana Marteles, Ana Pilar Gracia, Antonio Fernandez
Summary: A new coronavirus, SARS-CoV-2, emerged in Wuhan in 2019 and spread globally causing the pandemic COVID-19. Little is known about the impact of this virus on domestic and stray animals, especially cats. A study in Spain found that 3.51% of stray cats tested were seropositive to SARS-CoV-2, indicating their exposure to the virus for the first time. Additionally, concomitant infections with other pathogens like Toxoplasma and FIV were also identified.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Steven J. Berardinelli, Alexander Eletsky, Jessika Valero-Gonzalez, Atsuko Ito, Rajashri Manjunath, Ramon Hurtado-Guerrero, James H. Prestegard, Robert J. Woods, Robert S. Haltiwanger
Summary: This article investigates the mechanism of O-fucosylation modification of thrombospondin type-1 repeats (TSRs) in the endoplasmic reticulum (ER) quality control. Molecular dynamics simulations, crystallography, and NMR experiments provide evidence that the Glucose-Fucose disaccharide interacts with specific amino acids in the TSR3 domain, protecting a nearby disulfide bond. These findings reveal the importance of O-fucosylation modification in maintaining TSR stability.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Andres Manuel Gonzalez-Ramirez, Ana Sofia Grosso, Zhang Yang, Ismael Companon, Helena Coelho, Yoshiki Narimatsu, Henrik Clausen, Filipa Marcelo, Francisco Corzana, Ramon Hurtado-Guerrero
Summary: This study provides molecular insights into the function of C1GalT1, a glycosyltransferase that plays a key role in protein O-glycosylation. The crystal structure of the Drosophila enzyme-substrate complex reveals that C1GalT1 is an obligate GT-A fold dimer that follows a S(N)2 mechanism. The binding of glycopeptides to C1GalT1 is mainly driven by the GalNAc moiety, and the peptide sequence provides optimal kinetic and binding parameters. C1GalT1 recognizes a high-energy conformation of the alpha-GalNAc-Thr linkage to achieve glycosylation. These findings contribute to our understanding of glycosylation mechanisms adopted by glycosyltransferases.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Patricia Guerrero-Ochoa, Raquel Ibanez-Perez, German Berbegal-Pinilla, Diederich Aguilar, Isabel Marzo, Francisco Corzana, Martha Minjarez-Saenz, Javier Macias-Leon, Blanca Conde, Javier Raso, Ramon Hurtado-Guerrero, Alberto Anel
Summary: Two granulysin-based immunotoxins (SM3GRNLY and AR20.5GRNLY) were generated to target and induce cell death in Tn antigen-expressing tumor cells. The immunotoxins demonstrated stronger cell-killing effects compared to GRNLY alone and induced cell death through apoptotic, necroptotic, and necrotic mechanisms. In a xenograft model, the immunotoxins showed tumor-targeting ability and significantly reduced tumor volume. These findings highlight the potential of these immunotoxins as drugs for Tn-expressing cancers.
Article
Biochemistry & Molecular Biology
Conor W. Mitchell, Ignacy Czajewski, Daan M. F. van Aalten
Summary: This study used bioinformatic techniques to identify 22 candidate proteins that may be associated with OGT-CDG and found that these proteins are involved in various biological processes, including signal transduction, translational repression, cytoskeletal dynamics, and chromatin remodeling. Additionally, pathogenic variants associated with intellectual disability were identified at O-GlcNAcylation sites.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Victor Taleb, Qinghua Liao, Yoshiki Narimatsu, Ana Garcia-Garcia, Ismael Companon, Rafael Junqueira Borges, Andres Manuel Gonzalez-Ramirez, Francisco Corzana, Henrik Clausen, Carme Rovira, Ramon Hurtado-Guerrero
Summary: This study provides molecular insights into the interaction between mucinase AM0627 and O-glycans in gut bacteria. The enzyme specifically cleaves bis-T O-glycopeptides by recognizing both the sugar moieties and the peptide sequence. Structural comparison reveals a conserved residue responsible for the common activity of AM0627 and another mucinase with bis-T/Tn substrates.
NATURE COMMUNICATIONS
(2022)
Article
Veterinary Sciences
Sergio Villanueva-Saz, Marivi Martinez, Jacobo Giner, Ana Gonzalez, Ana Pilar Tobajas, Maria Dolores Perez, Erandi Lira-Navarrete, Andres Manuel Gonzalez-Ramirez, Javier Macias-Leon, Maite Verde, Andres Yzuel, Ramon Hurtado-Guerrero, Maykel Arias, Llipsy Santiago, Jordi Aguilo-Gisbert, Hector Ruiz, Delia Lacasta, Diana Marteles, Antonio Fernandez
Summary: The study finds that stray cats have a minimal role in the transmission of SARS-CoV-2, and there is no increase in seropositivity during different waves of COVID-19 outbreaks in this group of animals. Additionally, stray cats also have multiple co-infections including infectious peritonitis, heartworm disease, and feline immunodeficiency virus. Further epidemiological surveillance is needed to determine the risk that other animals may possess, even though stray cats do not seem to play a role in transmission.
VETERINARY RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Emma Scott, Kirsty Hodgson, Beatriz Calle, Helen Turner, Kathleen Cheung, Abel Bermudez, Fernando Jose Garcia Marques, Hayley Pye, Edward Christopher Yo, Khirul Islam, Htoo Zarni Oo, Urszula L. McClurg, Laura Wilson, Huw Thomas, Fiona M. Frame, Margarita Orozco-Moreno, Kayla Bastian, Hector M. Arredondo, Chloe Roustan, Melissa Anne Gray, Lois Kelly, Aaron Tolson, Ellie Mellor, Gerald Hysenaj, Emily Archer Goode, Rebecca Garnham, Adam Duxfield, Susan Heavey, Urszula Stopka-Farooqui, Aiman Haider, Alex Freeman, Saurabh Singh, Edward W. Johnston, Shonit Punwani, Bridget Knight, Paul McCullagh, John McGrath, Malcolm Crundwell, Lorna Harries, Denisa Bogdan, Daniel Westaby, Gemma Fowler, Penny Flohr, Wei Yuan, Adam Sharp, Johann de Bono, Norman J. Maitland, Simon Wisnovsky, Carolyn R. Bertozzi, Rakesh Heer, Ramon Hurtado Guerrero, Mads Daugaard, Janne Leivo, Hayley Whitaker, Sharon Pitteri, Ning Wang, David J. Elliott, Benjamin Schumann, Jennifer Munkley
Summary: Prostate cancer is the leading cancer among men, causing over 350,000 deaths worldwide annually. This study reveals that the glycosyltransferase enzyme GALNT7 is upregulated in prostate cancer tissue and can be used as a biomarker to diagnose the disease with higher accuracy than the traditional PSA test. Additionally, GALNT7 is found to play a role in promoting prostate tumor growth and is associated with cell cycle and immune signaling pathways. Overall, this study highlights the importance of GALNT7-mediated O-glycosylation in prostate cancer progression.
Review
Chemistry, Multidisciplinary
Ignacio Sanz-Martinez, Sandra Pereira, Pedro Merino, Francisco Corzana, Ramon Hurtado-Guerrero
Summary: N-acetylgalactosamine (GalNAc) type O-glycosylation is a crucial posttranslational modification in biology. Malfunction of this modification is associated with truncated O-glycans in cancer. Understanding the structure and recognition of GalNAc-containing glycopeptides can contribute to the development of therapeutic vaccines and new diagnostic tools for cancer detection.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Veterinary Sciences
Sergio Villanueva-Saz, Marivi Martinez, Pablo Rueda, Sara Bolea, Maria Dolores Perez, Maite Verde, Andres Yzuel, Ramon Hurtado-Guerrero, Julian Pardo, Llipsy Santiago, Antonio Fernandez, Maykel Arias
Summary: This study reports the detection and monitoring of SARS-CoV-2 antibodies in cats under natural conditions. The results show that these antibodies can persist for more than 16 months and reinfection is possible. The study confirms a gradual decrease in the immune response to SARS-CoV-2 in cats, but reinfection can stimulate an increase in immunity.
VETERINARY RESEARCH COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Edgar Gonzalez-Rodriguez, Mia Zol-Hanlon, Ganka Bineva-Todd, Andrea Marchesi, Mark Skehel, Keira E. Mahoney, Chloe Roustan, Annabel Borg, Lucia Di Vagno, Svend Kjaer, Antoni G. Wrobel, Donald J. Benton, Philipp Nawrath, Sabine L. Flitsch, Dhira Joshi, Andres Manuel Gonzalez-Ramirez, Katalin A. Wilkinson, Robert J. Wilkinson, Emma C. Wall, Ramon Hurtado-Guerrero, Stacy A. Malaker, Benjamin Schumann
Summary: The polybasic cleavage motif for the protease furin is a major factor in human viral transmission of SARS-CoV-2 spike. Variants of concern (VOCs) have extensive mutations in the region preceding this motif. Besides furin, spikes from these variants rely on other proteases such as TMPRSS2 for maturation. Glycans near the cleavage site have implications for proteolytic processing and the effects of variant-borne mutations.
ACS CENTRAL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Beatriz Piniello, Javier Macias-Leon, Shun Miyazaki, Ana Garcia-Garcia, Ismael Companon, Mattia Ghirardello, Victor Taleb, Billy Veloz, Francisco Corzana, Atsushi Miyagawa, Carme Rovira, Ramon Hurtado-Guerrero
Summary: In this study, the structures of soluble HMW1C-like N-glycosyltransferases (NGTs) were reported, revealing a key dyad of basic/acidic residues that plays a crucial role in Asn catalysis. The study also found that UDP-galactose and UDP-glucose mimetics act as poor substrates and inhibitors, impeding catalysis. QM/MM simulations provide insight into the reaction mechanism of AaNGT. These findings are important for understanding the mechanism of NGTs and designing drugs.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Collin J. Ballard, Miya R. Paserba, Earnest James Paul Daniel, Ramon Hurtado-Guerrero, Thomas A. Gerken
Summary: A large family of polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) play a crucial role in mucin O-glycosylation. The study reveals the importance of flanking charged residues in determining the substrate specificity of GalNAc-Ts. Different isoforms of GalNAc-Ts exhibit diverse charge specificities, and even isoforms with high sequence identity can have different charge preferences. These electrostatic interactions impact substrate binding and orientation on the enzyme surface, thus modulating their activities.
Article
Microbiology
Michael Wexler, Tal Zusman, Marika Linsky, Ziv Lifshitz, Gil Segal
Summary: In this study, the researchers investigated the core effectors of Legionella species and found that they generally perform the same function across different species. Specifically, three out of the nine core effectors in L. pneumophila were found to be required for maximal intracellular growth. The study also revealed that the non-translocated protein LegA3C physically interacts with LegA3 and is necessary for its conserved function.
CURRENT RESEARCH IN MICROBIAL SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Helena Coelho, Matilde de las Rivas, Ana S. Grosso, Ana Diniz, Catia O. Soares, Rodrigo A. Francisco, Jorge S. Dias, Ismael Companon, Lingbo Sun, Yoshiki Narimatsu, Sergey Y. Vakhrushev, Henrik Clausen, Eurico J. Cabrita, Jesus Jimenez-Barbero, Francisco Corzana, Ramon Hurtado-Guerrero, Filipa Marcelo
Summary: This study uses NMR spectroscopy and molecular modeling techniques to reveal the mechanisms of GalNAc-T2/T3/T4 isoforms in MUC1 O-glycosylation. The experiments show that the lectin domain plays an important role in site selection, and neighboring tandem repeats are critical for subsequent glycosylation. Additionally, specific salt bridges and inverse gamma-turn conformations in MUC1 are found to be key structural motifs for GalNAc-T4 specificity. In-cell analysis also demonstrates that GalNAc-T4 is the only isoform glycosylating the Thr of the immunogenic epitope PDTRP in vivo.