Review
Microbiology
Sabina Leanti La Rosa, Matthew P. Ostrowski, Arturo Vera-Ponce de Leon, Lauren S. McKee, Johan Larsbrink, Vincent G. Eijsink, Elisabeth C. Lowe, Eric C. Martens, Phillip B. Pope
Summary: This review summarizes recent insights into nutrient processing in microbiomes across different gastrointestinal ecosystems and discusses the implications for microbiome reprogramming to improve host health.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hayato Takihara, Shujiro Okuda
Summary: Interactions between humans and the gut microbiome involve supplying nutrients to gut epithelial cells and activating immunity. The gut microbiome is responsible for degrading plant-derived polysaccharides. We analyzed the distribution and abundance of glycan-related genes in the healthy human gut metagenome, showing large individual differences in abundance but similar distribution of gene classes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Oncology
Ishrat Rahman, Md Tanwir Athar, Mozaffarul Islam
Summary: Diabetes and cancer are closely related and may interact with each other. The complexity of these diseases mainly comes from various unwanted alterations, hindering the development of therapeutic agents.
FRONTIERS IN ONCOLOGY
(2021)
Article
Microbiology
Peter Spanogiannopoulos, Than S. Kyaw, Ben G. H. Guthrie, Patrick H. Bradley, Joyce Lee, Jonathan Melamed, Ysabella Noelle Amora Malig, Kathy N. Lam, Daryll Gempis, Moriah Sandy, Wesley Kidder, Erin L. Van Blarigan, Chloe E. Atreya, Alan Venook, Roy R. Gerona, Andrei Goga, Katherine S. Pollard, Peter J. Turnbaugh
Summary: Anti-cancer fluoropyrimidine drugs have antibacterial effects on the gut microbiome, and these drugs can be metabolized by gut bacteria via conserved pathways also found in mammalian hosts.
NATURE MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Chang Gu, Xin Shi, Xuening Dang, Jiafei Chen, Chunji Chen, Yumei Chen, Xufeng Pan, Tao Huang
Summary: This study analyzed common genes and pathways among different fibrotic diseases by collecting reported genes of eight fibrotic diseases and calculating KEGG and GO enrichment scores. Through comparison and analysis, key features and the common key molecule CTGF were identified to provide insights into the cellular and molecular mechanisms underlying fibrosis for potential drug development.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Yunqian Jin, Bin Wang, Lei Tian, Linxi Zhao, Shulei Guo, Hengchao Zhang, Lengrui Xu, Zanping Han
Summary: This study investigated the molecular mechanism associated with maize seed vigor by analyzing small RNAs and degradome sequencing. The results showed that maize seeds contain fewer miRNA families compared with animals, indicating a more synergistic function of miRNAs. Glycan degradation and galactose metabolism were found to be closely correlated with improved maize seed vigor.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Renjian Xie, Bifei Li, Lee Jia, Yumei Li
Summary: This study identified core genes and molecular mechanisms related to melanoma metastasis using gene expression profiles and bioinformatics analysis. Experimental validation showed that KRT5 plays an inhibitory role in melanoma metastasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Gastroenterology & Hepatology
Khanh Vu, Wendy Lou, Hein M. Tun, Theodore B. Konya, Nadia Morales-Lizcano, Radha S. Chari, Catherine J. Field, David S. Guttman, Rupasri Mandal, David S. Wishart, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Diana L. Lefebvre, Malcolm R. Sears, Stuart E. Turvey, Padmaja Subbarao, James A. Scott, Anita L. Kozyrskyj
Summary: The study found common mediators in the infant gut microbiome between child overweight and atopy following cesarean section and first pregnancy, notably the role of C difficile colonization.
Review
Biochemical Research Methods
Afnan M. Alnajeebi, Hend F. H. Alharbi, Walla Alelwani, Nouf A. Babteen, Wafa S. Alansari, Ghalia Shamlan, Areej A. Eskandrani
Summary: COVID-19 and lung cancer are complex and challenging diseases, and they may share some functions and functional components. Gene expression analysis and pathway enrichment can help us understand the relationships and common aberrations between them.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2022)
Article
Genetics & Heredity
Zhiyuan Yu, Chen Liang, Huaiyu Tu, Shuzhong Qiu, Xiaoyu Dong, Yonghui Zhang, Chao Ma, Peiyu Li
Summary: This study aimed to identify key genes and signaling pathways related to gastric cancer oncogenesis and progression using bioinformatics and meta-analysis methods. By integrating microarray datasets and conducting enrichment analyses and protein-protein interaction network construction, the study identified significant differentially expressed genes and hub genes associated with survival outcomes in gastric cancer.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Luz Maria Gonzalez-Castrillon, Maud Wurmser, Daniel Ohlund, Sara Ivy Wilson
Summary: The study extensively investigates the high nerve density in tumors and the role of nerves in metastasis, focusing on the molecular pathways and common features associated with PNI-associated cancers. The study identifies dysregulation of neurodevelopmental and axon guidance genes as common features in multiple cancers. These findings provide potential targets for novel cancer therapies and multi-cancer molecular biomarkers.
FRONTIERS IN GENETICS
(2023)
Article
Biology
Nasa Sinnott-Armstrong, Sahin Naqvi, Manuel Rivas, Jonathan K. Pritchard
Summary: GWAS are used to study the genetic basis of complex diseases and traits, and UK Biobank GWAS results for molecular traits like urate, IGF-1, and testosterone show easily interpretable hits near genes involved in relevant pathways. These molecular traits are highly polygenic, with thousands of variants contributing to trait variance across the genome.
Article
Microbiology
Nicholas A. Pudlo, Gabriel Vasconcelos Pereira, Jaagni Parnami, Melissa Cid, Stephanie Markert, Jeffrey P. Tingley, Frank Unfried, Ahmed Ali, Neha J. Varghese, Kwi S. Kim, Austin Campbell, Karthik Urs, Yao Xiao, Ryan Adams, Duna Martin, David N. Bolam, Dorte Becher, Emiley A. Eloe-Fadrosh, Thomas M. Schmidt, D. Wade Abbott, Thomas Schweder, Jan Hendrik Hehemann, Eric C. Martens
Summary: Gut bacteria have the ability to digest seaweed polysaccharides, and this adaptation is a result of gene exchange and metabolic plasticity in the human gut microbiome.
CELL HOST & MICROBE
(2022)
Article
Engineering, Environmental
Chen-Yu Zhao, Shaoguo Ru, Pengfei Cui, Xin Qi, Mayur B. Kurade, Swapnil M. Patil, Byong-Hun Jeon, Jiu-Qiang Xiong
Summary: This study investigated the ecotoxicological effects, biodegradation, and multiple metabolic pathways of enrofloxacin (ENR) by ryegrass, identifying key metabolic genes and proposing a biodegradation pathway. Results showed high removal rates of ENR by biodegradation and revealed the key functional genes involved in the degradation process. This study contributes to the understanding of antibiotic biodegradation in plants and highlights the potential of ryegrass in treating ENR-polluted water.
Article
Infectious Diseases
Jakob J. Malin, Christian J. H. von Wintersdorff, John Penders, Paul H. M. Savelkoul, Petra F. G. Wolffs
Summary: This study investigated the longitudinal fluctuations in prevalent antimicrobial resistance genes (ARGs) in non-travelling healthy volunteers and found that the abundance changes of prevalent ARGs were independent of travel behavior.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2023)
Article
Chemistry, Multidisciplinary
Spencer S. Macdonald, Jose H. Pereira, Feng Liu, Gregor Tegl, Andy DeGiovanni, Jacob F. Wardman, Samuel Deutsch, Yasuo Yoshikuni, Paul D. Adams, Stephen G. Withers
Summary: Researchers discovered a new glycoside phosphorylase (GP) through in silico sequence analysis and characterized its functionality and structure. This new GP synthesizes a previously undescribed biopolymer, expanding the possibilities for carbohydrate active enzyme research. The reverse phosphorolysis action of this GP provides an efficient method for enzymatically synthesizing the new biodegradable polymeric material.
ACS CENTRAL SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Feng Liu, Hong-Ming Chen, Zachary Armstrong, Stephen G. Withers
Summary: Azido sugars are frequently used in biological systems, but little attention has been paid to how well they represent the parent molecule. Glycosidases have been used as model enzyme systems to assess the accommodation of azides. Azides at secondary carbons are not well accommodated, while those at primary carbons are recognized by only a small subset of enzymes. Careful consideration should be given when using azide-modified sugars in research.
ACS CENTRAL SCIENCE
(2022)
Article
Chemistry, Physical
Yann Mathieu, Maria E. Cleveland, Harry Brumer
Summary: This study investigates the effect of deleting a specific loop in the active site of a Colletotrichum graminicola aryl alcohol oxidase on its catalytic activity, leading to changes in carbohydrate specificity and regiospecificity. The results highlight the catalytic adaptability of the mononuclear copper radical active site and provide a basis for designing improved biocatalysts for various applications.
Article
Biochemistry & Molecular Biology
Olivia Lui, Lharbi Dridi, Emmanuel Gonzalez, Suraya Yasmine, Ryszard Kubinski, Hannah Billings, Joerg Bohlmann, Stephen G. Withers, Corinne Maurice, Bastien Castagner
Summary: The effects of alpha-amylase inhibitors on glycan metabolism in human gut bacteria need further investigation.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Carmana Hunter, Zhizen Gao, Hong-Ming Chen, Nicole Thompson, Warren Wakarchuk, Mark Nitz, Stephen G. Withers, Lisa M. Willis
Summary: Sialic acids play a crucial role in cell function and targeting specific sialyl glycoforms on cell surfaces could be useful for biochemical tools and potential therapeutic interventions in chronic diseases. Although various strategies are being explored, there is currently no highly selective method for controlling cell surface sialosides targeting specific sialyl glycoforms.
ACS CHEMICAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Jessica K. Fong, Harry Brumer
Summary: The copper radical oxidases (CROs), represented by galactose 6-oxidase and glyoxal oxidase, are a diverse group of enzymes. They use oxygen as the final electron acceptor and have a unique tyrosine-cysteine co-factor for radical stabilization. Recent advancements in biochemistry and structural biology have expanded the understanding of CRO enzymology, biotechnology, and biology across different kingdoms of life.
ESSAYS IN BIOCHEMISTRY
(2023)
Article
Plant Sciences
Hila Behar, Yaseen Mottiar, Rohan Chandrasekhar, Allegra Corelli Grappadelli, Markus Pauly, A. Lacey Samuels, Shawn D. Mansfield, Harry Brumer
Summary: This study used a hybrid polar plant model, Populus alba x Populus grandidentata (P39), to investigate the expression, subcellular localization, and phenotypes and chemotypes of EG16-downregulated P39 plants. The results showed that Populus EG16 is strongly expressed in young tissues, but RNAi-mediated downregulation did not affect plant growth or the fine structure of hemicellulose xyloglucan, suggesting a restricted or currently unknown role in angiosperm physiology.
Article
Chemistry, Organic
Zi-Wang Wei, Haruka Niikura, Menghua Wang, Katherine S. Ryan
Summary: This study reports the biosynthetic gene cluster of Azaserine (1) from Glycomyces harbinensis and provides evidence from isotopic feeding, gene deletion, and biochemical experiments for a pathway involving hydrazinoacetic acid (2) and a peptidyl carrier protein-loaded serine (3) as intermediates to the final natural product 1.
Article
Multidisciplinary Sciences
Aiko Kurimoto, Seyed A. Nasseri, Camden Hunt, Mike Rooney, David J. Dvorak, Natalie E. LeSage, Ryan P. Jansonius, Stephen G. Withers, Curtis P. Berlinguette
Summary: The authors present an electrochemical method for cofactor regeneration without the need for supporting enzymes or mediators, nor the formation of NAD(2) dimers. They demonstrate that a bioelectrocatalytic palladium membrane reactor can be used to regenerate NADH from NAD(+) while bypassing the degradation of NAD(+) and optimizing conditions for enzymatic reactions.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Phillip G. Daniel-Ivad, Steven Van Lanen, Katherine S. Ryan
Summary: By using crystallography, we determined the crystal structure of Cap15, a nucleoside biosynthetic enzyme, which revealed the internal aldimine and the active site lysine. Our study also demonstrated how Cap15 catalyzes a stereoselective deprotonation reaction and identified active site residues that differentiate Cap15 from related enzymes. This work provides a structural basis for further investigation into the mechanism of this unique biosynthetic enzyme and sheds light on the emergence of oxygen reactivity in the SelA-like protein family.
Article
Chemistry, Multidisciplinary
Menghua Wang, Katherine S. Ryan
Summary: In this study, two new l-Alanosine-producing strains were discovered through genome mining. These strains lack the aspartate-nitrosuccinate pathway genes found in the original producer and use a unique set of nitrate-nitrite reductases to reduce nitrate instead. The repurposing of enzymes from the nitrogen cycle for specialized metabolite biosynthesis and the potential for the discovery of new nitric-oxide-derived natural products are demonstrated.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Jacob F. Wardman, Lyann Sim, Jennifer Liu, Teresa A. Howard, Andreas Geissner, Phillip M. Danby, Alisdair B. Boraston, Warren W. Wakarchuk, Stephen G. Withers
Summary: Mucin-type O-glycosylation is an important post-translational modification involved in cellular communication. However, the study of O-glycoproteins and O-glycans is challenging due to the lack of available enzymes for their assembly and degradation. To overcome this, a genetically encoded screening method was developed using engineered Escherichia coli to screen for enzymes that act on O-glycoproteins. The method uses an O-glycosylated fluorescence resonance energy transfer probe as a read-out of glycosylation state and can also assay glycosidases and glycosyltransferases. The methodology has potential for the directed evolution of O-glycopeptidases.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Zi-Wang Wei, Haruka Niikura, Kalindi D. Morgan, Condurache M. Vacariu, Raymond J. Andersen, Katherine S. Ryan
Summary: This study demonstrates the adenylation and incorporation mechanism of piperazic acid (Piz) into nonribosomal peptides, as well as the consensus sequences for piperazic acid adenylation. The fusion protein of piperazate synthase and adenylation domain suggests a close biosynthetic relationship between piperazic acid formation and its adenylation. These findings shed light on the evolution of biosynthetic systems for the activation of free piperazic acid.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Eden Kaddouch, Maria E. Cleveland, David Navarro, Sacha Grisel, Mireille Haon, Harry Brumer, Mickael Lafond, Jean-Guy Berrin, Bastien Bissaro
Summary: This study presents a simple method for direct measurement of galactose oxidase (GalOx) activity by identifying galactosylated oxidized products using high-performance anion-exchange chromatography coupled to pulsed amperometric detection (HPAEC-PAD). The results showed that this method is more sensitive than other methods.
Article
Biochemistry & Molecular Biology
Lyann Sim, Nicole Thompson, Andreas Geissner, Stephen G. Withers, Warren W. Wakarchuk
Summary: The prospect of producing human-like glycoproteins in bacteria as an alternative to costly mammalian cell expression systems is attractive. By engineering an E. coli strain and introducing mammalian sialyltransferases, high-yielding production of human interferon alpha 2b and human growth hormone with sialic acid glycans has been achieved.