Article
Clinical Neurology
Jack M. Shireman, Fatemeh Atashi, Gina Lee, Eunus S. Ali, Miranda R. Saathoff, Cheol H. Park, Sol Savchuk, Shivani Baisiwala, Jason Miska, Maciej S. Lesniak, C. David James, Roger Stupp, Priya Kumthekar, Craig M. Horbinski, Issam Ben-Sahra, Atique U. Ahmed
Summary: Glioblastoma is a primary brain cancer with a near 100% recurrence rate. A molecular circuit involving the interaction between ARL13B and IMPDH2 has been identified, which affects the efficacy of chemotherapy.
Review
Biochemistry & Molecular Biology
Vidhi Pareek, Anthony M. Pedley, Stephen J. Benkovic
Summary: This review highlights the human de novo purine biosynthetic pathway, discussing the assembly and function of purinosomes, as well as potential signaling pathways that regulate their formation and disassembly. The findings support the existence of a metabolon and suggest insights into how other metabolic pathways may be organized for optimal function.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Antoine Gedeon, Gouzel Karimova, Nour Ayoub, Julien Dairou, Quentin Giai Gianetto, Sophie Vichier-Guerre, Pierre-Olivier Vidalain, Daniel Ladant, Helene Munier-Lehmann
Summary: In this study, the protein-protein interactions network among the enzymes involved in de novo purine nucleotide biosynthesis in Escherichia coli was characterized using a bacterial two-hybrid approach. The results showed a dense network of interactions connecting most enzymes, with PurK as one of the central hubs. Mutations in PurK disrupted multiple interactions in the network, leading to changes in purine nucleotide pools and bacterial fitness. These findings indicate that bacterial de novo purine nucleotide biosynthesis enzymes can form a supramolecular complex, and proper interactions within this complex are crucial for bacterial fitness.
Article
Microbiology
Meng-Yu Liu, Li-Xiao Sun, Hui Qian, Yun-Ran Zhang, Xue-Ming Zhu, Lin Li, Shuang Liang, Jian-Ping Lu, Fu-Cheng Lin, Xiao-Hong Liu
Summary: The study revealed the importance of de novo purine nucleotide biosynthesis in conidiation, development, and pathogenicity in M. oryzae.
Article
Multidisciplinary Sciences
Xiaozeng Mi, Chun Yang, Dahe Qiao, Mengsha Tang, Yan Guo, Sihui Liang, Yan Li, Zhengwu Chen, Juan Chen
Summary: Tea plants have economic, health, and cultural value. Transcriptome analysis of a tea resource in SDT revealed significantly different metabolite characteristics compared to 'Qiancha 1'. The study provides candidate genes for understanding the synthesis mechanisms of these metabolites and for molecular breeding of tea plants.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Simon Miranda, Jorge Lagreze, Anne-Sophie Knoll, Andrea Angeli, Richard Espley, Andrew P. Dare, Mickael Malnoy, Stefan Martens
Summary: In this study, researchers identified putative 3-hydroxylases in two wild Malus species that are capable of producing sieboldin, a specialised secondary metabolite of the dihydrochalcone group. They also discovered key residues mutations in the CYP98A protein of wild accessions that allow it to accept the substrate phloretin, leading to sieboldin accumulation. These findings provide important insights into the biosynthesis of sieboldin in Malus species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Endocrinology & Metabolism
Cecilie Melau, John E. Nielsen, Signe Perlman, Lene Lundvall, Lea Langhoff Thuesen, Kristine Juul Hare, Mette Schou Hammerum, Hanne Frederiksen, Rod T. Mitchell, Anders Juul, Anne Jorgensen
Summary: Human fetal adrenal tissue was successfully cultured ex vivo to study adrenal steroidogenesis, demonstrating the potential for investigating pharmaceutical exposures or therapeutic options targeting imbalanced steroidogenesis in adrenal disorders such as CAH.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2021)
Article
Multidisciplinary Sciences
Vinod Kumar, Krishnakumar Sugumaran, Amwaj Al-Roumi, Anisha Shajan
Summary: This study analyzed the transcriptomes of hydroponically grown lettuce under different LED lighting conditions using next-generation sequencing. The results showed that blue and red light treatments had the highest number of differentially expressed transcripts. The differentially expressed genes under different light qualities were mainly involved in stress response, nucleosome assembly, oxidation-reduction process, and response to water deprivation.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Jun-Zhang Zhao, Wei Wang, Tao Liu, Lei Zhang, De-Zheng Lin, Jia-Yin Yao, Xiang Peng, Gang Jin, Tian-Tian Ma, Jin-Bo Gao, Fang Huang, Jun Nie, Qing Lv
Summary: This study reveals that MYBL2 regulates purine synthesis and promotes HCC progression by transcriptionally activating IMPDH1, suggesting it could be a potential candidate for targeted therapy for HCC.
Article
Agriculture, Multidisciplinary
Shizhong Li, Chaoning Liang, Guoxia Liu, Jian-Ming Jin, Yong Tao, Shuang-Yan Tang
Summary: Engineering an artificial microbial community for natural product production is a promising strategy. The polyculture approach using recombinant Escherichia coli strains showed superior performance in de novo chlorogenic acid (CGA) biosynthesis, compared to previously reported methods, by avoiding metabolic flux competition and balancing module proportions.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Yong Ding, Xinli Li, Geoff P. Horsman, Pengwei Li, Min Wang, Jine Li, Zhilong Zhang, Weifeng Liu, Bian Wu, Yong Tao, Yihua Chen
Summary: Nicotinamide adenine dinucleotide (NAD(+)) is a crucial molecule in biological processes and a de novo quinolinic acid pathway, named the C3N pathway, has been discovered as an alternative route for NAD(+) biosynthesis. The C3N pathway shows potential in cofactor engineering and higher production of desired compounds in cell factories.
Article
Biotechnology & Applied Microbiology
Osakina Aron, Frankine Jagero Otieno, Ibrahim Tijjani, Zifeng Yang, Huxiao Xu, Shuning Weng, Jiayuan Guo, Songmao Lu, Zonghua Wang, Wei Tang
Summary: This study identified and characterized the functions of MoAde4, an orthologue of yeast Ade4 in Magnaporthe oryzae. The results demonstrated that MoAde4 plays a crucial role in fungal development and pathogenicity, suggesting it as a suitable target for antifungal development against recalcitrant plant fungal pathogens.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Shimeng Tan, Yanying Chen, Guoying Zhou, Junang Liu
Summary: The study compared the pathogenicity of Colletotrichum fructicola from different geographic populations on oil tea leaf tissue and gene expression differences, finding that strains from Wuzhishan exhibited stronger pathogenicity, potentially attributable to greater regulation of the purine metabolism pathway.
Article
Cardiac & Cardiovascular Systems
Qian Ma, Qiuhua Yang, Jiean Xu, Xiaoyu Zhang, David Kim, Zhiping Liu, Qingen Da, Xiaoxiao Mao, Yaqi Zhou, Yongfeng Cai, Vidhi Pareek, Ha Won Kim, Guangyu Wu, Zheng Dong, Wen-Liang Song, Lin Gan, Chunxiang Zhang, Mei Hong, Stephen J. Benkovic, Neal L. Weintraub, David Fulton, John M. Asara, Issam Ben-Sahra, Yuqing Huo
Summary: This study reveals the important role of de novo purine synthesis in VSMC proliferation in arterial disease and suggests that targeting ATIC could be a promising therapeutic approach.
Article
Biotechnology & Applied Microbiology
Dandan Li, Qing Wang, Songshu Chen, Hongchang Liu, Keqin Pan, Jinling Li, Chunli Luo, Hualei Wang
Summary: This study investigated the transcriptome sequencing of rhizomes at different ages, revealing the link between polysaccharides and saponin biosynthesis and gene expression in Polygonatum cyrtonema Hua. It identified key enzymes and genes involved in polysaccharide and saponin biosynthesis and validated the results through quantitative real-time PCR. The findings provide insights into the genetic engineering of P. cyrtonema to increase the content of major active ingredients.
Review
Microbiology
Stephanie L. Collins, Jonathan C. Stine, Jordan E. Bisanz, C. Denise Okafor, Andrew D. Patterson
Summary: This Review discusses host-microbiota interactions and their impact on bile acid metabolism and composition. The gut microbiota plays a crucial role in bile acid metabolism, with diverse biological roles for bile acids being discovered. External factors such as antibiotics and diet also influence bile acid composition. Understanding the impact of bile acid signaling networks in different organs is increasingly important for the development of targeted therapeutics.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Le Thi My Le, James Robert Thompson, Sepehr Dehghani-Ghahnaviyeh, Shashank Pant, Phuoc Xuan Dang, Jarrod Bradley French, Takahisa Kanikeyo, Emad Tajkhorshid, Amer Alam
Summary: Phospholipid extrusion by ABC subfamily A (ABCA) exporters is essential for cellular physiology, but the molecular details of substrate interactions and transport mechanisms are still not well understood. In this study, cryo-EM structures of lipid-embedded human ABCA7 in different states were determined, revealing the structural framework for substrate entry and exit from ABCA7 and providing insights into the underlying conformational transitions. Combining functional analysis and molecular dynamics simulations, the study also shed light on lipid partitioning and localized membrane perturbations that contribute to ABCA7 function and may have implications for other ABCA family transporters.
Article
Biochemistry & Molecular Biology
Sougat Misra, Tai-Jung Lee, Aswathy Sebastian, John McGuigan, Chang Liao, Imhoi Koo, Andrew D. Patterson, Randall M. Rossi, Molly A. Hall, Istvan Albert, K. Sandeep Prabhu
Summary: Macrophages play a crucial role in inflammation and its resolution. Selenium and selenoproteins, which contain the amino acid selenocysteine, are essential for the functions of macrophages. In this study, the researchers investigated the role of SELENOW, a highly expressed selenoprotein, in inflammation using Selenow knock-out macrophages. The results suggest that SELENOW is involved in redox processes and bioenergetics during inflammation and its resolution.
Article
Biochemistry & Molecular Biology
Jonathan A. A. Young, Silvana Duran-Ortiz, Stephen Bell, Kevin Funk, Yuan Tian, Qing Liu, Andrew D. D. Patterson, Edward O. O. List, Darlene E. E. Berryman, John J. J. Kopchick
Summary: Growth hormone (GH) affects protein metabolism and alters circulating levels of glycine and hydroxyproline. GH abnormality, such as increased GH action or GH resistance, leads to changes in amino acid concentrations in plasma and feces. Acute GH treatment decreases liver gene expression of glycine metabolism genes and serum glycine in mice.
Article
Biochemistry & Molecular Biology
Fangcong Dong, Iain A. Murray, Andrew Annalora, Denise M. Coslo, Dhimant Desai, Krishne Gowda, Jian Yang, Dingbowen Wang, Imhoi Koo, Fuhua Hao, Shantu G. Amin, Andrew D. Patterson, Craig Marcus, Gary H. Perdew
Summary: A certain diet can enhance the activity of the aryl hydrocarbon receptor (AHR) in the intestinal tract, which is responsible for maintaining intestinal barrier homeostasis. This is possibly achieved through the role of certain dietary substrates as CYP1A1/1B1 substrates, which increase the half-life of potent AHR ligands. The gut bacterial metabolite urolithin A (UroA) has been identified as one of these substrates, and its intake can lead to increased AHR activity in key barrier tissues.
Review
Biochemistry & Molecular Biology
Matthew J. Binder, Anthony M. Pedley
Summary: Fluctuations in nutrient and biomass availability impact cell survival and proliferation, and cells adapt to these changes by adjusting their metabolic networks. Molecular chaperones, including Hsp90 and Hsp70, have been found to influence metabolic processes by altering enzymatic activities and metabolite flux. This article summarizes the role of chaperones in human metabolic enzymes and their supramolecular assemblies, highlighting their involvement in enzymatic activity regulation, metabolite flux modulation, and enzyme translocation and degradation.
Review
Biochemistry & Molecular Biology
Anika Zaman, Jarrod B. French, Nick Carpino
Summary: The Sts proteins, Sts-1 and Sts-2, play important roles in regulating signaling pathways. Sts-1 possesses protein tyrosine phosphatase activity and is involved in regulating multiple signaling pathways. Sts-2 has lower catalytic activity and its signaling role is less studied.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Dari Shalon, Rebecca Neal Culver, Jessica A. Grembi, Jacob Folz, Peter V. Treit, Handuo Shi, Florian A. Rosenberger, Les Dethlefsen, Xiandong Meng, Eitan Yaffe, Andres Aranda-Diaz, Philipp E. Geyer, Johannes B. Mueller-Reif, Sean Spencer, Andrew D. Patterson, George Triadafilopoulos, Susan P. Holmes, Matthias Mann, Oliver Fiehn, David A. Relman, Kerwyn Casey Huang
Summary: This study developed an ingestible device that can collect samples from multiple regions of the human intestinal tract during normal digestion. Multi-omics analysis of the collected samples revealed significant differences in bacteria, phages, host proteins, and metabolites between the intestines and stool. The study provides insights into the roles of the gut microbiome and metabolome in human physiology and disease through non-invasive longitudinal profiling of microorganisms, proteins, and bile acids along the intestinal tract.
Article
Biochemistry & Molecular Biology
Kafi K. J. Belfon, Nandini Sharma, Rachael Zigweid, Madison Bolejack, Doug Davies, Thomas E. Edwards, Peter J. Myler, Jarrod B. French
Summary: Differences in purine metabolism between microbes and humans can be exploited for the development of antimicrobial therapies. We have solved crystal structures of the PurE enzyme from human pathogens and identified several new inhibitors that selectively target microbial PurE enzymes.
Article
Oncology
Sangshan Tian, Devendra Paudel, Fuhua Hao, Rabin Neupane, Rita Castro, Andrew D. Patterson, Amit K. Tiwari, K. Sandeep Prabhu, Vishal Singh
Summary: This study reveals that supplementation of diet with refined inulin leads to abnormal succinate accumulation in the intestinal lumen, which contributes to promoting colon inflammation and tumorigenesis.
Article
Cell Biology
Beng San Yeoh, Rachel M. Golonka, Piu Saha, Mrunmayee R. Kandalgaonkar, Yuan Tian, Islam Osman, Andrew D. Patterson, Andrew T. Gewirtz, Bina Joe, Matam Vijay-Kumar
Summary: Congenital portosystemic shunt (PSS) occurs sporadically in C57BL/6 J mice, leading to abnormal serologic, metabolic, and physiologic parameters. To reliably and efficiently identify PSS mice, we explored simple, inexpensive, and noninvasive urine-based screening tests. Metabolome profiling revealed elevated levels of Krebs cycle intermediates in the urine of PSS mice, which we utilized to develop three colorimetric assays: urinary iron-chelation, pH strip, and phenol red assays. These assays provide a feasible and noninvasive method for diagnosing PSS in mice, aiding biomedical research by stratifying PSS mice and minimizing confounding factors.
Article
Neurosciences
Fangcong Dong, Andrew J. Annalora, Iain A. Murray, Yuan Tian, Craig B. Marcus, Andrew D. Patterson, Gary H. Perdew
Summary: The aryl hydrocarbon receptor (AHR) plays important roles in xenobiotic metabolism, immune function, and tissue homeostasis. The regulation of AHR activity by endogenous ligands is still poorly understood. In this study, we identified and quantified 6 tryptophan metabolites that individually activate AHR in mouse and human serum. These metabolites are not significantly metabolized by CYP1A1/1B1, unlike the potent endogenous AHR ligand 6-formylindolo[3,2b]carbazole. Our results suggest that these tryptophan metabolites may contribute to constitutive but low level systemic AHR activity in humans.
INTERNATIONAL JOURNAL OF TRYPTOPHAN RESEARCH
(2023)
Article
Neurosciences
Ethan W. Morgan, Fangcong Dong, Andrew J. Annalora, Iain A. Murray, Trenton Wolfe, Reece Erickson, Krishne Gowda, Shantu G. Amin, Kristina S. Petersen, Penny M. Kris-Etherton, Craig B. Marcus, Seth T. Walk, Andrew D. Patterson, Gary H. Perdew
Summary: The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that regulates various cellular functions. Tryptophan metabolites derived from host and bacterial metabolism act as AHR activators. This study investigates the presence and metabolic source of these metabolites and examines the biological relevance of circulating tryptophan metabolites. The results improve our understanding of homeostatic AHR activity and related diseases.
INTERNATIONAL JOURNAL OF TRYPTOPHAN RESEARCH
(2023)
Article
Gastroenterology & Hepatology
Alexis Bretin, Jun Zou, Beng San Yeoh, Vu L. Ngo, Shawn Winer, Daniel A. Winer, Lavanya Reddivari, Michael Pellizzon, William A. Walters, Andrew D. Patterson, Ruth Ley, Benoit Chassaing, Matam Vijay-Kumar, Andrew T. Gewirtz
Summary: Psyllium protects against experimental colitis by altering bile acid metabolism and activating FXR, which suppresses pro-inflammatory signaling.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gary H. Perdew, Charlotte Esser, Megan Snyder, David H. Sherr, Ellen H. van den Bogaard, Karen McGovern, Pedro M. Fernandez-Salguero, Xavier Coumoul, Andrew D. Patterson
Summary: The aryl hydrocarbon receptor (AHR) senses low-molecular-weight molecule signals from environmental exposures, the microbiome, and host metabolism. It plays important roles in host homeostasis, chronic disease development, and responses to toxic insults. Recent research has shown that AHR is a promising target for cancer, metabolic diseases, skin conditions, and autoimmune disease. This meeting aimed to explore the potential therapeutic applications based on our understanding of this receptor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)