Review
Biochemistry & Molecular Biology
Rajesh Narasimamurthy, David M. Virshup
Summary: In our modern society, the consequences of disrupting our circadian rhythms by skipping or delaying sleep are severe, leading to various disorders. The internal clock is regulated by the reversible phosphorylation of PERIOD proteins, controlled by isoforms of casein kinase 1 (CK1). Through biochemical, genetic, and structural studies, a better understanding of how the core clock is regulated has been achieved, opening new approaches for clock regulation.
Article
Plant Sciences
Xijuan Zhao, Huiling Zhang, Tengfei Liu, Yanan Zhao, Xinxi Hu, Shengxuan Liu, Yuan Lin, Botao Song, Changzheng He
Summary: In this study, transcriptome analysis was performed on the tubers of the purple-turning potato variety RM-210 during anthocyanin accumulation. The StMYBA1 gene was found to be continuously upregulated during this process and showed a strong correlation with the structural genes CHS and CHI. Overexpression of StMYBA1 gene was found to promote anthocyanin accumulation and the expression of structural genes in potato leaves, suggesting that StMYBA1 gene activates the expression of structural genes to promote potato anthocyanin biosynthesis under light conditions.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Xun Sun, H. Jane Dyson, Peter E. Wright
Summary: The phosphorylation of Thr55 modulates DNA binding of p53, controlling both activation and termination of p53-mediated transcriptional programs during different stages of the cellular DNA damage response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis
Summary: REBASE is a comprehensive database of information about restriction-modification (RM) system components, providing details on recognition and cleavage sites for restriction enzymes and DNA methyltransferases, their commercial availability, sensitivity to methylation, crystal and sequence data. The database is regularly updated and can be accessed through a website and FTP.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
David B. Langley, Peter Schofield, Damien Nevoltris, Jennifer Jackson, Katherine J. L. Jackson, Tim J. Peters, Melanie Burk, Jacqueline M. Matthews, Antony Basten, Christopher C. Goodnow, Sheryl van Nunen, Joanne H. Reed, Daniel Christ
Summary: Humans produce anti-alpha-gal antibodies in response to various immunogens, and this study reveals a common binding motif in these antibodies which is associated with a specific genetic factor. Additionally, the introduction of this binding motif into certain antibody libraries allows for the rapid selection of alpha-gal binders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Pil-Won Seo, Andreas Hofmann, Jun-Ha Kim, Seung-A Hwangbo, Jun-Hong Kim, Ji-Won Kim, Thi Yen Ly Huynh, Hyon E. Choy, Soo-Jung Kim, Jimin Lee, Jie-Oh Lee, Kyeong Sik Jin, Suk-Youl Park, Jeong-Sun Kim
Summary: Type I restriction-modification enzymes are composed of methylation, DNA sequence-recognition, and restriction subunits. In this study, the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with DNA-mimicking Ocr protein and SAH was determined. The reconstructed structure of the MTase dimer revealed its symmetry and conformational flexibility in recognizing DNA regions. This study provides insights into the structural characteristics of Type I restriction-modification enzymes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Multidisciplinary Sciences
Nabil Azhar, Rami A. Namas, Khalid Almahmoud, Akram Zaaqoq, Othman A. Malak, Derek Barclay, Jinling Yin, Fayten El-Dehaibi, Andrew Abboud, Richard L. Simmons, Ruben Zamora, Timothy R. Billiar, Yoram Vodovotz
Summary: The study analyzed time course data on multiple inflammatory mediators in the blood of blunt trauma patients and proposed a new control architecture for systemic inflammation. A logical model was created to test this hypothesis, predicting key qualitative features of systemic inflammation in patient sub-groups.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Weijun Jiang, Jiajia Shi, Jingjie Zhao, Qiu Wang, Dan Cong, Fenghua Chen, Yu Zhang, Yuhan Liu, Junzheng Zhao, Qian Chen, Linhao Gu, Wenjia Zhou, Chenhang Wang, Zhaoyuan Fang, Shuhui Geng, Wei Xie, Luo-Nan Chen, Yang Yang, Yun Bai, Haodong Lin, Xiajun Li
Summary: ZFP57 is a master regulator of genomic imprinting, which controls the expression of target imprinted genes by maintaining differential DNA methylation at ICRs. Mutations in Zfp57 lead to allelic expression switches in target imprinted genes and genes associated with the NOTCH signaling pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Kosuke Koyama, Yui Mikawa, Shota Nakagawa, Ryota Kurashiki, Takashi Ohshiro, Hirokazu Suzuki
Summary: Geobacillus thermodenitrificans K1041, a highly transformable thermophile, has been characterized in this study. An optimized electroporation procedure was developed to enhance its acceptance of Escherichia coli-derived plasmids, making it a promising host for screening genetic libraries at elevated temperatures. The organism exhibited swarming motility and rapid growth at 60 degrees C. Moreover, it efficiently accepted methylation-controlled plasmids, suggesting circumvention of a restriction-modification system. It also showed substantial plasmid-directed production of heterologous proteins. The draft genomic sequence revealed the presence of genes involved in restriction-modification systems. A Delta resA mutant with enhanced transformation efficiencies was generated. Overall, this study provides new insights into the biological and genomic properties of Geobacillus thermodenitrificans K1041 and its potential as a host for genetic library screening.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Annie Shao, Micah D. Gearhart, Siu Chiu Chan, Zhen Miao, Katalin Susztak, Peter Igarashi
Summary: The transcription factor HNF-1 beta plays a crucial role in the normal development of the kidney and other epithelial organs by directly regulating the expression of multiple axon guidance genes. Dysregulation of these genes may underlie kidney defects in HNF-1 beta mutant mice.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Qi Long, Kai Yan, Chendong Wang, Yanling Wen, Furong Qi, Hui Wang, Peng Shi, Xingguo Liu, Wai-Yee Chan, Xuemei Lu, Hui Zhao
Summary: Increasing evidence shows that interspecific hybridization plays a crucial role in speciation, but chromatin compatibility issues often hinder this process. Genomic imbalances, such as chromosomal DNA loss and rearrangements, lead to infertility in hybrids. The mechanism behind reproductive isolation in interspecific hybridization remains unknown. In this study, it was found that the modification of maternally defined H3K4me3 in Xenopus laevis and Xenopus tropicalis hybrids determines the fate of the hybrids, with texls showing developmental arrest and lexts being viable. Transcriptomic analysis revealed that the P53 pathway is overactivated and the Wnt signaling pathway is suppressed in texls hybrids. Furthermore, the lack of maternal H3K4me3 disrupts gene expression balance between the L and S subgenomes in texls hybrids. Attenuation of p53 can delay the arrested development of texls. This study proposes an additional model of reproductive isolation based on modifications of maternally defined H3K4me3.
Article
Plant Sciences
Ping Wang, Xiao Liang, Hanmo Fang, Jiao Wang, Xiaotian Liu, Yimei Li, Kai Shi
Summary: Pipecolic acid (Pip) and N-hydroxypipecolic acid (NHP) accumulate during fruit ripening, and mutating the biosynthesis-related genes Slald1 and Slfmo1 in tomato fruits results in delayed ripening, decreased fruit size, nutrition, and flavor. Exogenous treatment with Pip and NHP promotes fruit ripening and improves fruit quality.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Wenqing Zhou, Lei Zhou, Jordan Zhou, Coco Chu, Chao Zhang, Robbyn E. Sockolow, Gerard Eberl, Gregory F. Sonnenberg
Summary: This study defines ROR gamma t(+) immune cells in the intestine at single-cell resolution and identifies a subset of ILC3s that expresses ZBTB46, a transcription factor shared with conventional dendritic cells. ZBTB46 restrains the inflammatory properties of ILC3s and plays a non-redundant role in orchestrating intestinal health.
Article
Microbiology
Kun Zhang, Yucheng Zhang, Yunash Maharjan, Febri Gunawan Sugiokto, Jun Wan, Renfeng Li
Summary: The study elucidates the role of RNA methylation at the N6 position of adenosine in biological processes, identifies the relationship between YTHDF2 and caspases, and investigates its mechanism in EBV replication.
Review
Microbiology
Alexandra L. Krause, Timothy P. Stinear, Ian R. Monk
Summary: This review highlights the lag in molecular biology research on Enterococcus faecalis and Enterococcus faecium compared to other Gram-positive pathogens and discusses methods to overcome barriers in DNA transfer. Improving transformation techniques will expedite our understanding of these important pathogens.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Chemistry, Multidisciplinary
Erika Erickson, Thomas J. Shakespeare, Felicia Bratti, Bonnie L. Buss, Rosie Graham, McKenzie A. Hawkins, Gerhard Koenig, William E. Michener, Joel Miscall, Kelsey J. Ramirez, Nicholas A. Rorrer, Michael Zahn, Andrew R. Pickford, John E. McGeehan, Gregg T. Beckham
Summary: This study compares the performance of two types of PET-hydrolyzing enzymes and finds that reaction temperature has the strongest influence on their performance. Both enzymes achieve higher levels of PET conversion for substrates with moderate crystallinity, and show different inhibition profiles to product accumulation.
Article
Biotechnology & Applied Microbiology
Eugene Kuatsjah, Christopher W. Johnson, Davinia Salvachua, Allison Z. Werner, Michael Zahn, Caralyn J. Szostkiewicz, Christine A. Singer, Graham Dominick, Ikenna Okekeogbu, Stefan J. Haugen, Sean P. Woodworth, Kelsey J. Ramirez, Richard J. Giannone, Robert L. Hettich, John E. McGeehan, Gregg T. Beckham
Summary: The study demonstrates that replacing PobA with PraI, which has a broader cofactor preference, can increase muconic acid yield, reduce 4-HBA accumulation, enhance NADPH utilization, and alleviate metabolic bottleneck, leading to improved production of value-added products from lignin-derived compounds.
METABOLIC ENGINEERING
(2022)
Article
Multidisciplinary Sciences
William M. Kincannon, Michael Zahn, Rita Clare, Jessica Lusty Beech, Ari Romberg, James Larson, Brian Bothner, Gregg T. Beckham, John E. McGeehan, Jennifer L. DuBois
Summary: Several bacteria possess catabolic pathways for PET degradation, which are crucial for genetically engineering microbes for PET upcycling. TPADO is an important enzyme in these pathways, and its structural and biochemical characteristics have been elucidated in this study. TPADO exhibits strong substrate selectivity for TPA and shows significant differences in structure and activity compared to other known enzymes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Chemistry, Physical
Erika Erickson, Alissa Bleem, Eugene Kuatsjah, Allison Z. Werner, Jennifer L. DuBois, John E. McGeehan, Lindsay D. Eltis, Gregg T. Beckham
Summary: The application of microbes in converting aromatic compounds derived from lignin is a rapidly growing research field, which may lead to the production of valuable bio-based chemicals from this otherwise difficult to utilize resource. Enzymes play a crucial role in the catabolism of aromatic compounds, and understanding their mechanisms provides opportunities for efficient biological conversion.
Article
Chemistry, Multidisciplinary
Richard K. Brizendine, Erika Erickson, Stefan J. Haugen, Kelsey J. Ramirez, Joel Miscall, Davinia Salvachua, Andrew R. . Pickford, Margaret J. Sobkowicz, John E. McGeehan, Gregg T. Beckham
Summary: Enzymatic depolymerization of PET is a potential method for PET recycling, but extensive thermomechanical preprocessing is often conducted. In this study, the effect of PET particle size and crystallinity on the performance of a specific enzyme was investigated using different types of PET. The results show that particle size reduction can increase the reaction rate for high-crystallinity PET, but has little effect on the overall conversion extent. Amorphization of PET is necessary for enzymatic PET recycling, while particle size reduction may not be required.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Review
Environmental Sciences
Lucy C. M. Omeyer, Emily M. Duncan, Kornrawee Aiemsomboon, Nicola Beaumont, Sujaree Bureekul, Bin Cao, Luis R. Carrasco, Suchana Chavanich, James R. Clark, Muhammad R. Cordova, Fay Couceiro, Simon M. Cragg, Neil Dickson, Pierre Failler, Gianluca Ferraro, Stephen Fletcher, Jenny Fong, Alex T. Ford, Tony Gutierrez, Fauziah Shahul Hamid, Jan G. Hiddink, Pham T. Hoa, Sophie I. Holland, Lowenna Jones, Nia H. Jones, Heather Koldewey, Federico M. Lauro, Charlotte Lee, Matt Lewis, Danny Marks, Sabine Matallana-Surget, Claudia G. Mayorga-Adame, John McGeehan, Lauren F. Messer, Laura Michie, Michelle A. Miller, Zeeda F. Mohamad, Nur Hazimah Mohamed Nor, Moritz Miller, Simon P. Neill, Sarah E. Nelms, Deo Florence L. Onda, Joyce J. L. Ong, Agamuthu Pariatamby, Sui C. Phang, Richard Quilliam, Peter E. Robins, Maria Salta, Aida Sartimbul, Shiori Shakuto, Martin W. Skov, Evelyn B. Taboada, Peter A. Todd, Tai Chong Toh, Suresh Valiyaveettil, Voranop Viyakarn, Passorn Wonnapinij, Louisa E. Wood, Clara L. X. Yong, Brendan J. Godley
Summary: Southeast Asia is considered to have high levels of marine plastic pollution, and it is important to understand its impacts and risks to marine ecosystems in order to develop mitigation measures. An international network of experts from various countries has set a research agenda for marine plastic pollution in the region, identifying key themes and research questions. Understanding the fate, degradation, and impacts of marine plastic pollution is crucial for tackling the issue effectively in Southeast Asia and providing insights for the rest of the world.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Abril Gijsbers, Mathias Eymery, Ye Gao, Isabella Menart, Vanesa Vinciauskaite, Dritan Siliqi, Peter J. Peters, Andrew McCarthy, Raimond B. G. Ravelli
Summary: Pathogenic species from the Mycobacterium genus use specialized secretion systems (ESX-1 to ESX-5) to transport virulence factors across their cell envelope, influencing immune response and cell death. This study presents the crystal structure of Mycobacterium tuberculosis ESX-1 secretion-associated substrate EspB bound to its chaperone EspK, revealing a mechanism for the secretion of EspB in Mycobacterium species.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Erika Erickson, Japheth E. Gado, Luisana Avilan, Felicia Bratti, Richard K. Brizendine, Paul A. Cox, Raj Gill, Rosie Graham, Dong-Jin Kim, Gerhard Koenig, William E. Michener, Saroj Poudel, Kelsey J. Ramirez, Thomas J. Shakespeare, Michael Zahn, Eric S. Boyd, Christina M. Payne, Jennifer L. DuBois, Andrew R. Pickford, Gregg T. Beckham, John E. McGeehan
Summary: This study expands the number and diversity of thermotolerant scaffolds for enzymatic PET deconstruction by using bioinformatics and machine learning to mine 74 putative thermotolerant PET hydrolases. The study identifies new PET-active biocatalysts and discovers protein folds and accessory domains associated with PET deconstruction.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Luisana Avilan, Bruce R. Lichtenstein, Gerhard Koenig, Michael Zahn, Mark D. Allen, Liliana Oliveira, Matilda Clark, Victoria Bemmer, Rosie Graham, Harry P. Austin, Graham Dominick, Christopher W. Johnson, Gregg T. Beckham, John E. McGeehan, Andrew R. Pickford
Summary: Enzyme-based depolymerization is a viable approach for recycling PET, but the concentration-dependent inhibition of IsPETase hinders its effectiveness. This study finds that the inhibition depends on incubation time, solution conditions, and PET surface area. Furthermore, this inhibition is also observed in other mesophilic PET-degrading enzymes, but not in the highly thermostable HotPETase. This work highlights the limitations of using natural mesophilic hydrolases for PET hydrolysis and the potential benefits of enhancing their thermostability.
Article
Cell Biology
Ana Popovic, Mitro Miihkinen, Sujan Ghimire, Rafael Saup, Max L. B. Gronloh, Neil J. Ball, Benjamin T. Goult, Johanna Ivaska, Guillaume Jacquemet
Summary: Using GFP-Trap and BioID combined with mass spectrometry, we identified lamellipodin (RAPH1) as a novel cargo of MYO10. The FERM domain of MYO10 is required for RAPH1 localization and accumulation at filopodia tips. Surprisingly, the MYO10-binding site on RAPH1 is not within its adhesome interaction domains, but instead located in a conserved helix after the pleckstrin homology domain.
JOURNAL OF CELL SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Kevin J. McNaught, Eugene Kuatsjah, Michael Zahn, Erica T. Prates, Huiling Shao, Gayle J. Bentley, Andrew R. Pickford, Josephine N. Gruber, Kelley V. Hestmark, Daniel A. Jacobson, Brenton C. Poirier, Chen Ling, Myrsini San Marchi, William E. Michener, Carrie D. Nicora, Jacob N. Sanders, Caralyn J. Szostkiewicz, Dusan Velickovic, Mowei Zhou, Nathalie Munoz, Young-Mo Kim, Jon K. Magnuson, Kristin E. Burnum-Johnson, K. N. Houk, John E. McGeehan, Christopher W. Johnson, Gregg T. Beckham
Summary: Deciphering the mechanisms of bacterial fatty acid biosynthesis is crucial for both engineering bacterial hosts and developing antibiotics. This study reveals that Pseudomonas putida KT2440 has three distinct pathways for initiating fatty acid biosynthesis, with the third pathway being a novel alternative. The findings provide new opportunities for various biotechnological and biomedical applications.
METABOLIC ENGINEERING
(2023)
Article
Chemistry, Physical
Alissa Bleem, Eugene Kuatsjah, Gerald N. Presley, Daniel J. Hinchen, Michael Zahn, David C. Garcia, William E. Michener, Gerhard Konig, Konstantinos Tornesakis, Marco N. Allemann, Richard J. Giannone, John E. McGeehan, Gregg T. Beckham, Joshua K. Michener
Summary: This study identified a Rieske-type guaiacol O-demethylase, GdmA, and its reductase partner GdmB in Novosphingobium aromaticivorans. The GdmAB combination showed high efficiency in guaiacol turnover, providing new options for microbial conversion of lignin-derived substrates.
Article
Chemistry, Physical
Rosie Graham, Erika Erickson, Richard K. Brizendine, Davinia Salvachua, William E. Michener, Yaohao Li, Zhongping Tan, Gregg T. Beckham, John E. McGeehan, Andrew R. Pickford
Summary: Enzymes with multi-domain architectures are often found in nature and have been shown to enhance the degradation ability of polymers like PET. However, this study suggests that accessory binding modules are not necessary for cost-effective enzymatic PET recycling in industrial applications.
Article
Chemistry, Multidisciplinary
Taylor Uekert, Jason S. DesVeaux, Avantika Singh, Scott R. Nicholson, Patrick Lamers, Tapajyoti Ghosh, John E. McGeehan, Alberta C. Carpenter, Gregg T. Beckham
Summary: This study conducted a process-based life cycle assessment (LCA) to evaluate the enzymatic PET recycling system for a closed-loop PET recycling scheme. The results showed that enzymatic PET recycling performed worse than virgin TPA and PET production in most impact categories, but improvements in the recycling process could reduce its overall environmental impacts to levels equivalent to virgin production.
Article
Chemistry, Multidisciplinary
Jessica Lusty Beech, Rita Clare, William M. Kincannon, Erika Erickson, John E. McGeehan, Gregg T. Beckham, Jennifer L. DuBois
Summary: Esterase enzymes play important roles in various hydrolysis reactions. This study presents a UV/visible assay for the real-time quantification of ester hydrolysis. The method offers an accurate and cost-effective route for high-throughput screening and kinetic measurements of esterases.