Article
Microbiology
Anke Chen, Dan Wang, Rui Ji, Jixi Li, Shaohua Gu, Rong Tang, Chaoneng Ji
Summary: In this study, a thermostable beta-glucosidase (TsBGL) was isolated and characterized from the Thermoprotei Thermofilum sp. ex4484_79, exhibiting high activity and specific activity at elevated temperatures and pH levels. The crystal structure of TsBGL reveals a classical (alpha/beta)(8)-barrel catalytic domain, with catalytic sites including Glu210 and Glu414. TsBGL shows promise for potential industrial applications with its high thermostability and catalytic activity.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Tomohiko Matsuzawa, Masahiro Watanabe, Yusuke Nakamichi, Hironaga Akita, Katsuro Yaoi
Summary: This paper reports the crystal structures of Metagenomic MeBglD2 complexed with various saccharides, revealing its substrate recognition mechanism. The subsite -1 of MeBglD2 is structurally similar to other GH1 enzymes, but the binding modes of the positive subsites vary depending on the type of sugar. Three residues (Glu183, Asn227, and Asn229) located at the positive subsites of MeBglD2 are involved in substrate specificity in the presence of additive sugars. Docking simulation suggests that Asn229 and Trp329 play key roles in recognizing the +1 D-glucose in cellobiose.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Pashupati Bhandari, Jeffrey P. Tingley, David R. J. Palmer, D. Wade Abbott, Janet E. Hill
Summary: Gardnerella species in the vaginal microbiome play a key role in glycogen metabolism, utilizing predicted amylase enzymes to break down glycogen and release glucose.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Microbiology
Nurfatini Radzlin, Amira Suriaty Yaakop, Kian Mau Goh, Kok Jun Liew, Iffah Izzati Zakaria, Ummirul Mukminin Kahar
Summary: This study reports the isolation of a halophilic marine bacterial strain PS-C1 from Sekinchan beach in Selangor, Malaysia, which belongs to the genus Celeribacter. The genome analysis of PS-C1 revealed the presence of multiple industrially important glycoside hydrolase (GH) genes. The activities of two GHs (beta-glucosidase and licheninase) were demonstrated, suggesting that strain PS-C1 could be a potential source of novel GH enzymes for lignocellulosic biomass degradation.
Article
Agriculture, Multidisciplinary
Ju-Hee Cha, Minsun Hong, Chang-Jun Cha
Summary: In this study, a fungal beta-glycosidase belonging to subfamily 4 of GH family 30 (GH30) was characterized with hydrolysis and transglycosylation activities towards various substrates, representing the first fungal beta-glycosidase with transglycosylation activities in subfamily 4 of GH30.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Shumao Chai, Xueliang Zhang, Yuejiao Gao, Lishuang Nie, Chenchen Xiang, Mingming Cao, Shaochen Wang, Zhiyang Feng
Summary: A novel endo-/β-1,4-glucanase ZFYN1413-87 with strong enzyme activity was identified and studied in this research, showing 52% retained activity even after treatment in pH 3.0 buffer for 2 hours, representing a unique example in the GH6 family.
CARBOHYDRATE RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Kanyisa Ndata, Walter Nevondo, Bongi Cekuse, Leonardo Joaquim van Zyl, Marla Trindade
Summary: In this study, a novel beta-xylosidase XylP81 from the poorly studied GH39 family was discovered, which exhibits overall kinetic properties similar to other bacterial GH39 beta-xylosidases but shows unusually high tolerance to products, making it a promising candidate for industrial applications.
Article
Chemistry, Medicinal
Dianyi Li, Zheng Wang, Yong Yu, Huirong Li, Wei Luo, Bo Chen, Guoqing Niu, Haitao Ding
Summary: A novel GH2 beta-galactosidase from Marinomonas sp. BSi20584 was successfully expressed in E. coli and showed stable soluble form. The purified enzyme had a specific activity of 96.827 U mg(-1) at 30 degrees C using ONPG as a substrate. It had an optimum pH of 7.0 and an optimum temperature of 50 degrees C. The enzyme's activity was enhanced by some divalent cations and inhibited by EDTA. Despite being derived from a cold-adapted strain, the enzyme exhibited considerable stability against various physical and chemical elements. It also showed activity towards rare substrates. The enzyme is a promising candidate for the industrial application of beta-galactosidase.
Article
Biochemistry & Molecular Biology
In Jung Kim, Uwe T. Bornscheuer, Ki Hyun Nam
Summary: In this study, the biochemical and structural analysis of a Bgl enzyme (TsaBgl) from the hemicellulose-degrading bacterium Thermoanaerobacterium saccharolyticum was reported. TsaBgl exhibited maximum hydrolase activity at pH 6.0 and 55°C and showed a unique structure compared to other known Bgls. The study improved our understanding of the inhibition and glucose tolerance mechanisms of Bgl enzymes, which is crucial for their industrial application.
Article
Agriculture, Multidisciplinary
Laura Plaza-Vinuesa, Oswaldo Hernandez-Hernandez, Ana Sanchez-Arroyo, Jose M. Cumella, Nieves Corzo, Ana M. Munnoz-Labrador, F. Javier Moreno, Blanca de las Rivas, Rosario Munoz
Summary: This study confirmed the myrosinase-like activity of Lactiplantibacillus plantarum WCFS1, indicating that glucosinolates in this strain may undergo phosphorylation and the glycosidases belonging to the GH1 family are involved in the hydrolysis of phosphorylated glucosinolates.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Microbiology
Julia A. Bockwoldt, Matthias A. Ehrmann
Summary: Levilactobacillus (L.) brevis TMW 1.2112 is capable of producing 1,3-β-D-glucan, a capsular exopolysaccharide (EPS), from activated sugar nucleotide precursors. The genome analysis of L. brevis TMW 1.2112 revealed the presence of glycoside hydrolases (GH) enzymes. The beta-glucosidase BglB showed high affinity towards its substrate, but had low hydrolytic activity towards the EPS produced by L. brevis TMW 1.2112. Phylogenetic analysis of GH 3 beta-glucosidases from other lactic acid bacteria (LAB) suggested that these enzymes are likely exo-active and not directly associated with EPS production.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Nicholas G. S. McGregor, Joan Coines, Valentina Borlandelli, Satoko Amaki, Marta Artola, Alba Nin-Hill, Daniel Linzel, Chihaya Yamada, Takatoshi Arakawa, Akihiro Ishiwata, Yukishige Ito, Gijsbert A. van der Marel, Jeroen D. C. Codee, Shinya Fushinobu, Herman S. Overkleeft, Carme Rovira, Gideon J. Davies
Summary: The discovery of zinc-dependent retaining glycoside hydrolases presents unresolved mechanistic questions, particularly the controversy surrounding the proposed mechanism involving a zinc-coordinated cysteine nucleophile and a thioglycosyl enzyme intermediate. A synthesized beta-l-arabinofuranosidase inhibitor reacts exclusively with the cysteine thiol catalytic nucleophiles of GH families 127 and 146, supporting further research into the breakdown of the thioglycosyl enzyme intermediate. X-ray crystal structures and simulations provide insight into the mechanisms of zinc-coordinated cysteine as the catalytic nucleophile and the energetics of this unique metalloenzyme clan.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Stefanie Neun, Paul Brear, Eleanor Campbell, Theodora Tryfona, Kamel El Omari, Armin Wagner, Paul Dupree, Marko Hyvonen, Florian Hollfelder
Summary: The abundance of protein sequence data is not matched by the number of experimentally verified functional annotations. In this study, we used high-throughput microfluidic droplet screening to identify a new beta-glucuronidase enzyme with little homology to previously studied enzymes. This finding demonstrates the potential of functional metagenomics in uncovering the function of enzymes that cannot be predicted by bioinformatics.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tomoya Ota, Wataru Saburi, Linda Elizabeth Jewell, Tom Hsiang, Ryozo Imai, Haruhide Mori
Summary: In this study, a GH3 beta-glucosidase (MnBG3A) from Microdochium nivale was identified and characterized. MnBG3A showed activity on d-glucoside and slight activity on d-xyloside. Compared to beta-glucosidases from Aspergillus spp., MnBG3A has similar features but higher sensitivity to inhibitory effects.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2023)
Review
Agriculture, Multidisciplinary
Michael Kotik, Natalia Kulik, Katerina Valentova
Summary: Flavonoids and their glycosides are abundant in plant-based foods and studying the glycosylation process is important for understanding their bioactivities and applications.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Kai Deng, Xi Wang, Nicole Ing, Paul Opgenorth, Markus de Raad, Jinho Kim, Blake A. Simmons, Paul D. Adams, Anup K. Singh, Taek Soon Lee, Trent R. Northen
Summary: We developed a novel mass spectrometry-based assay that allows rapid quantification of primary alcohols produced by cell cultures. This assay combines TEMPO-based oxidation chemistry and oxime ligation, followed by product analysis using Nanostructure-Initiator Mass Spectrometry. It can accurately monitor C5 to C18 alcohols, as well as glucose and gluconate in the growth medium, which is crucial for strain characterization and optimization. The assay shows comparable results to gas chromatography for isoprenol production but requires significantly less acquisition time per sample. By applying this assay, we gained new insights into the utilization of alcohols by P. Putida and found that this strain had limited growth on heptanol and octanol.
ANALYTICAL BIOCHEMISTRY
(2023)
Review
Biochemical Research Methods
Hector G. Martin, Tijana Radivojevic, Jeremy Zucker, Kristofer Bouchard, Jess Sustarich, Sean Peisert, Dan Arnold, Nathan Hillson, Gyorgy Babnigg, Jose M. Marti, Christopher J. Mungall, Gregg Beckham, Lucas Waldburger, James Carothers, ShivShankar Sundaram, Deb Agarwal, Blake A. Simmons, Tyler Backman, Deepanwita Banerjee, Deepti Tanjore, Lavanya Ramakrishnan, Anup Singh
Summary: Self-driving labs combine fully automated experiments with AI, bringing a new paradigm to scientific research. While there are functioning SDLs in chemistry and materials science, synthetic biology offers unique opportunities due to the genome as a single target for affecting biological cell behavior. However, investment in biological SDLs should be directed towards solving difficult and enabling biological questions. Here, challenges and opportunities in creating SDLs for synthetic biology are discussed.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Microbiology
Mee-Rye Park, Rahul Gauttam, Bonnie Fong, Yan Chen, Hyun Gyu Lim, Adam M. Feist, Aindrila Mukhopadhyay, Christopher J. Petzold, Blake A. Simmons, Steven W. Singer
Summary: The study of pentose sugar catabolism in the P. putida group revealed inherent diversity, which provides alternative hosts for biomass conversion.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Dorothee Liebschner, Nigel W. Moriarty, Billy K. Poon, Paul D. Adams
Summary: In macromolecular crystallographic structure refinement, the creation of geometric restraints for ligands is challenging due to their chemical variability, novel nature, and specific interactions with protein binding pockets. Quantum-mechanical approaches can accurately determine ligand geometries, but are hindered by the flexibility of molecules with multiple minima. To overcome these issues, the Quantum Mechanical Restraints (QMR) procedure optimizes ligand geometry in situ, considering the influence of the macromolecule on ligand energy minima. QMR restraints generally result in lower deviations from target stereochemistry compared to conventionally generated restraints, especially for accurate torsion restraints.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Physical
Brandon J. Bloomer, Sean N. Natoli, Marc Garcia-Borras, Jose H. Pereira, Derek B. B. Hu, Paul D. Adams, K. N. Houk, Douglas S. Clark, John F. Hartwig
Summary: Artificial metalloenzymes (ArMs), containing synthetic metal cofactors, are widely used as biocatalysts for unnatural reactions. However, detailed mechanistic information on the effects of protein scaffold on ArM structure and reactivity is limited. This study presents the structure of an unnatural P450 analogue and kinetic analysis of its reaction, revealing a mechanism initiated by cofactor conformational change and highlighting the influence of cofactor dynamics on the catalytic reaction of ArMs.
Article
Plant Sciences
Vanessa Brisson, Courtney Swink, Jeffrey Kimbrel, Xavier Mayali, Ty Samo, Suzanne M. Kosina, Michael Thelen, Trent R. Northen, Rhona K. Stuart
Summary: The roles of different ecological classes of algal exometabolites in regulating microbial community composition are not well understood. In this study, we identified exometabolites from the diatom Phaeodactylum tricornutum and investigated their potential to influence bacterial abundances. We found that secretion of selective bacterial growth substrates represents one mechanism by which algal exometabolites can modulate bacterial community composition.
Article
Multidisciplinary Sciences
Rachelle Davenport, Benjamin P. Bowen, Laurel M. Lynch, Suzanne M. Kosina, Itamar Shabtai, Trent R. Northen, Johannes Lehmann
Summary: Soil organic matter (SOM) is composed of reactive carbon molecules that impact SOM formation and persistence. Microbial decomposition drives variability in the molecular diversity of SOM across ecosystems, with ecosystem type and soil horizon being significant factors. Microbial degradation in the soil profile has a greater influence on the molecular diversity of SOM than environmental factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Jing Dai, Kiera B. Wilhelm, Amanda J. Bischoff, Jose H. Pereira, Michel T. Dedeo, Derek M. Garcia-Almedina, Paul D. Adams, Jay T. Groves, Matthew B. Francis
Summary: Photosynthetic light harvesting requires efficient energy transfer within dynamic networks of light-harvesting complexes embedded within phospholipid membranes. Artificial light-harvesting models are valuable tools for understanding the structural features underpinning energy absorption and transfer within chromophore arrays. Here, a method for attaching a protein-based light-harvesting model to a planar, fluid supported lipid bilayer (SLB) is developed.
Article
Multidisciplinary Sciences
Brian C. Sanders, Suman Pokhrel, Audrey D. Labbe, Irimpan I. Mathews, Connor J. Cooper, Russell B. Davidson, Gwyndalyn Phillips, Kevin L. Weiss, Qiu Zhang, Hugh O'Neill, Manat Kaur, Jurgen G. Schmidt, Walter Reichard, Surekha Surendranathan, Jyothi Parvathareddy, Lexi Phillips, Christopher Rainville, David E. Sterner, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W. Moriarty, Paul D. Adams, Andrzej Joachimiak, Brett L. Hurst, Suresh Kumar, Tauseef R. Butt, Colleen B. Jonsson, Lori Ferrins, Soichi Wakatsuki, Stephanie Galanie, Martha S. Head, Jerry M. Parks
Summary: Designed a series of protease inhibitors targeting SARS-CoV-2, with the most effective inhibitor capable of blocking viral replication in mammalian cells and showing no significant inhibition of human proteases. These findings present an opportunity for the development of protease inhibitors.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Pavel V. Afonine, Paul D. Adams, Alexandre G. Urzhumtsev
Summary: Diffraction intensities in crystallographic experiments come from the entire crystal unit cell, including the macromolecule, its surrounding solvent, and other compounds. A single atomic model cannot adequately describe the contributions from disordered solvent, semi-ordered solvent, and disordered polymer loops. This study proposes an efficient solution for modeling these complex components, which are implemented in the computational crystallography toolbox (CCTBX) and Phenix software.
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2023)
Article
Biochemical Research Methods
Thomas C. Terwilliger, Pavel Afonine, Dorothee Liebschner, Tristan Croll, Airlie J. McCoy, Robert D. Oeffner, Christopher J. Williams, Billy K. Poon, Jane S. Richardson, Randy J. Read, Paul D. Adams
Summary: Experimental structure determination can be accelerated with AI-based structure-prediction methods like AlphaFold, which can produce electron-density maps and structural models using sequence information and crystallographic data. By iterating through cycles of structure prediction, a predicted model can be used as a template for prediction in subsequent cycles. This study applied the procedure to X-ray data for 215 structures and achieved a high accuracy, with 87% of the models matching those in the database. It is concluded that AlphaFold predictions based on sequence information alone are usually accurate enough for solving the crystallographic phase problem, and a general strategy for structure determination that includes AI-based prediction is suggested.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Correction
Biochemical Research Methods
P. V. Afonine, R. W. Grosse-Kunstleve, P. D. Adams, A. Urzhumtsev
Summary: Equations in Sections 2.3 and 2.4 of the article by Afonine et al. have been corrected.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Plant Sciences
Qing Zheng, Yuntao Hu, Suzanne M. Kosina, Marc W. Van Goethem, Susannah G. Tringe, Benjamin P. Bowen, Trent R. Northen
Summary: Biocrusts, phototroph-driven communities in arid soil, have beneficial interactions with cyanosphere bacteria similar to those in the rhizosphere. This study found that biocrust microbes promote the growth of a model grass and a dominant biocrust cyanobacterium, and identified specific strains that significantly promote the growth of both hosts. Furthermore, a metabolite produced by one of the strains increased the biomass of the model grass. These findings indicate that biocrusts and diverse photoautotrophic hosts can be a source for new plant growth-promoting microbes and metabolites.
Article
Biochemical Research Methods
Pavel V. Afonine, Oleg V. Sobolev, Nigel W. Moriarty, Thomas C. Terwilliger, Paul D. Adams
Summary: Refining atomic models at low resolution is challenging due to lack of detailed experimental data. Using restraints on Ramachandran plots or residue side-chain rotameric states as refinement targets is not ideal. Therefore, finding alternative model-validation criteria is desirable.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Ecology
Shwetha M. Acharya, Mon Oo Yee, Spencer Diamond, Peter F. Andeer, Nameera F. Baig, Omolara T. Aladesanmi, Trent R. Northen, Jillian F. Banfield, Romy Chakraborty
Summary: To understand the composition and function of rhizosphere microbiomes, it is important to study individual roots in standardized growth containers. The microbial community in different zones of the root (tip and base) of young Brachypodium distachyon grown in natural soil was analyzed, and it was found that Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria were significantly enriched in the rhizosphere. However, there was no difference in microbial composition between root tips and root base or across different growth containers.
ISME COMMUNICATIONS
(2023)