Article
Biochemistry & Molecular Biology
Sudhaker Dharavath, Khushboo Kumari, Sudhir Kumar, Samudrala Gourinath
Summary: This study reveals the mechanism of insensitivity of serine acetyltransferase EhSAT3 to L-cysteine and identifies the crucial role of the C-terminal region in regulating feedback inhibition.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Automation & Control Systems
Hanfeng Li, Xianfu Zhang, Shuai Liu
Summary: This article proposes an improved dynamic gain method for studying the global regulation problem of feedforward nonlinear systems. The method improves the convergence speed of the system state by designing a controller with a dynamic gain using a new time-varying function. The advantages of the improved dynamic gain method are illustrated through a simulation example.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2022)
Article
Automation & Control Systems
Hua Zhang, Fujin Jia, Junwei Lu
Summary: This paper studies the global output regulation problem for nonlinear output feedback affine systems with unknown functions and unmeasured states. By proposing a Lemma and designing a control scheme based on backstepping method, the paper solves the global output regulation problem of nonlinear systems and the "explosion of terms" problem of backstepping.
INTERNATIONAL JOURNAL OF SYSTEMS SCIENCE
(2022)
Review
Cell Biology
Yinfeng Xu, Wei Wan
Summary: This review summarizes the importance of acetylation modifications in the regulation of autophagy and their regulatory roles on multiple autophagy proteins. Acetylation regulates autophagy initiation, autophagosome formation, and transcriptional regulation by targeting core protein complexes and key regulatory molecules.
Article
Multidisciplinary Sciences
Jin Meng, Ling Fu, Keke Liu, Caiping Tian, Ziyun Wu, Youngeun Jung, Renan B. Ferreira, Kate S. Carroll, T. Keith Blackwell, Jing Yang
Summary: The study provides a comprehensive assessment of cysteine reactivity and oxidative modifications in C. elegans, shedding light on redox signaling at the organismal level.
NATURE COMMUNICATIONS
(2021)
Article
Automation & Control Systems
Debao Fan, Xianfu Zhang, Weihao Pan
Summary: This article focuses on the global regulation problem for a class of large-scale nonlinear systems with unknown growth rate and unknown external disturbances. A novel decentralized output-feedback switching control method is proposed to offset the uncertainties. The method combines logic-based switching technique and gain scaling technique, allowing for instant adjustment of controller parameters and demonstrating strong adaptive capability and disturbance tolerance. The effectiveness of the proposed control method is verified through two examples, including an engineering feedback control system design example.
INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL
(2023)
Article
Automation & Control Systems
Min-Sung Koo, Ho-Lim Choi
Summary: This paper addresses a regulation problem for a class of feedforward nonlinear systems with unknown control coefficients and unknown growth rate. By considering time-varying control coefficients and constructing a Lyapunov function, a new adaptive controller is derived to overcome the difficulties caused by uncertain nonlinearities and unknown ranges of the control coefficients. The system analysis and simulation results of a numerical example are provided to verify the effectiveness of the proposed control method.
JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS
(2023)
Article
Automation & Control Systems
Ahmet Taha Koru, Selahattin Burak Sarsilmaz, Tansel Yucelen, Eric Norman Johnson
Summary: This study focuses on the global design of internal model-based distributed dynamic state feedback control and presents a solution with proven existence through structured Lyapunov inequality. A comparison of the proposed global design method with local design methods is made through numerical examples.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2021)
Article
Biochemistry & Molecular Biology
Yinxiao Wang, Fengping Du, Yingbo Li, Juan Wang, Xiuqin Zhao, Zhikang Li, Jianlong Xu, Wensheng Wang, Binying Fu
Summary: N-6-methyladenosine (m6A) methylation plays a role in regulating rice responses to salt stress. m6A methylation is significantly increased in shoots under salt stress, and there are differential m6A sites in shoots and roots. These differential sites are regulated in a tissue-specific manner and may mediate salt tolerance through transcription regulation, ROS homeostasis, and auxin signaling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Julia Sindlinger, Stefan Schoen, Juergen Eirich, Soren Kirchgaessner, Iris Finkemeier, Dirk Schwarzer
Summary: The researchers developed a series of peptide probes conjugated with different amino acid-CoA for studying NAT complex interactome. The results showed that these peptide probes could separate different subunits and provide insights into substrate specificity, demonstrating their usefulness in studying NAT complex interactome in physiological and pathological backgrounds.
Article
Multidisciplinary Sciences
Ce Bian, Zhao Jing, Hong Wang, Lixin Wu, Zhaohui Chen, Bolan Gan, Haiyuan Yang
Summary: A new paper by Bian and colleagues reveals that oceanic mesoscale eddies are the main driver of marine heatwave (MHW) life cycles over most parts of the global ocean. Utilizing a historical simulation from a global eddy-resolving climate model, the study demonstrates that heat flux convergence by these eddies plays a dominant role in the growth and decay of MHWs. This research emphasizes the importance of understanding the role of mesoscale eddies in controlling global MHWs and the need for eddy-resolving ocean models in accurate MHW forecasts.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Qingmei Zeng, Kun Wang, Yongxiang Zhao, Qingzhi Ma, Zhinan Chen, Wan Huang
Summary: p300 acts as a transcription coactivator and an acetyltransferase that plays a crucial role in tumourigenesis and progression. It has been proven to regulate various pathophysiological processes and function as an acetyltransferase that drives malignant tumours. In addition, p300 is involved in posttranslational modifications that promote malignant biological behaviors.
Article
Cell Biology
Xiangpeng Dai, Xiaoling Zhang, Qing Yin, Jia Hu, Jianping Guo, Yang Gao, Aidan H. Snell, Hiroyuki Inuzuka, Lixin Wan, Wenyi Wei
Summary: This study reveals that the acetyltransferase p300 activates BRAF kinase by promoting BRAF K601 acetylation, which plays a significant role in melanoma and is associated with resistance to BRAF(V600E) inhibitors.
Article
Biochemical Research Methods
Di Zhang, Sophia Hsin-Jung Li, Christopher G. King, Ned S. Wingreen, Zemer Gitai, Zhiyuan Li
Summary: Translational regulation plays a critical role in the mismatch between mRNA level and protein abundance in bacteria. By quantifying gene-specific translational regulations under carbon, nitrogen, and phosphate limitations in Escherichia coli, this study reveals a diversity of translational regulations cooperating with transcriptional regulations. Codon usage partially predicts a gene's cross-condition variability in translation efficiency. These findings broaden the understanding of translational regulation under different environments and provide novel strategies for synthetic biology.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Cell Biology
Jian Feng, Teng Zhang, Oceane Sorel, Wen Meng, Xinquan Zhang, Zhao Lai, Weiming Yuan, Yidong Chen, Yufei Huang, Shou-Jiang Gao
Summary: This study reveals the important role of N-6-methyladenosine (m(6)A) in regulating innate immunity against bacterial and viral infections. By examining cellular m(6)A epitranscriptomes, the study shows that many innate immune response genes undergo m(6)A modifications. The findings provide valuable resources for the scientific community.
CELL DEATH & DISEASE
(2022)
Article
Chemistry, Medicinal
Jonathan H. Shrimp, Yihang Jing, Supuni Thalalla Gamage, Kathryn M. Nelson, Joseph Han, Keri M. Bryson, David C. Montgomery, Justin M. Thomas, Kellie D. Nance, Sunny Sharma, Stephen D. Fox, Thorkell Andressen, Wilson R. Sinclair, Hong Wu, Abdellah Allali-Hassani, Guillermo Senisterra, Masoud Vedadi, Denis Lafontaine, Jayme L. Dahlin, Ronen Marmorstein, Michael A. Walters, Jordan L. Meier
Summary: Remodelin, a putative small molecule inhibitor of RNA acetyltransferase NAT10, was found to be a cryptic assay interference compound that interacts with multiple protein targets in cells and does not affect the formation of ac4C. Biophysical analyses did not show direct evidence of interaction between remodelin and the NAT10 acetyltransferase active site.
ACS MEDICINAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Yihang Jing, Jose L. Montano, Michaella Levy, Jeffrey E. Lopez, Pei-Pei Kung, Paul Richardson, Krzysztof Krajewski, Laurence Florens, Michael P. Washburn, Jordan L. Meier
Summary: Chemical proteomics offers a powerful strategy for high-throughput assignment of enzyme function or inhibitor selectivity, but optimizing probes for specific enzyme family members and distinguishing signals from background noise remain challenging. This study introduces a physiochemical discernment strategy based on the CoA cofactor for improving chemical proteomics, demonstrating its efficacy in identifying optimized pulldown probes and comparing its selectivity against traditional competitive methods. The use of CoA-based chemoproteomic probes is validated in evaluating the specificity of small molecule acetyltransferase inhibitors, showcasing their potential in drug discovery.
ACS CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yihang Jing, Sarah E. Bergholtz, Anthony Omole, Rhushi A. Kulkarni, Thomas T. Zengeya, Euna Yoo, Jordan L. Meier
Summary: This study presents a new chemical strategy for synthesizing a stable isostere of malonyllysine, which can mimic features of endogenous lysine modification and be used for tool development and functional analysis. The isostere shows resistance to thermal decarboxylation and can be recognized by anti-malonyllysine antibodies and histone deacylases.
Article
Chemistry, Multidisciplinary
David Bartee, Kellie D. Nance, Jordan L. Meier
Summary: This study reports the synthesis and biophysical characterization of ac4C in its endogenous eukaryotic sequence context, establishing a chemical foundation for understanding the function of a universally conserved nucleobase in biology and disease.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Courtney N. Link, Supuni Thalalla Gamage, Diamond Gallimore, Robert Kopajtich, Christine Evans, Samantha Nance, Stephen D. Fox, Thorkell Andresson, Raj Chari, Joseph Ivanic, Holger Prokisch, Jordan L. Meier
Summary: Chemical modification of cytidine in noncoding RNAs is important for translation regulation and disease. However, the distribution and dynamics of these modifications are still unknown due to a lack of sensitive sequencing technologies. In this study, a protonation-dependent sequencing reaction is developed to detect 5fC and 5caC in RNA, enhancing the reactivity and sensitive detection of these modified cytidine residues. This method provides a molecular foundation for studying the role of oxidized RNA cytidine residues in diseases.
Meeting Abstract
Biochemistry & Molecular Biology
Samantha R-A Nance, Jordan L. Meier, Raj Chari, Christine N. Evans
Article
Biochemistry & Molecular Biology
Mary T. Doan, Michael D. Neinast, Erika L. Varner, Kenneth C. Bedi, David Bartee, Helen Jiang, Sophie Trefely, Peining Xu, Jay P. Singh, Cholsoon Jang, J. Eduardo Rame, Donita C. Brady, Jordan L. Meier, Kenneth B. Marguiles, Zoltan Arany, Nathaniel W. Snyder
Summary: Research has shown that mammals can synthesize a six-carbon compound through the metabolism of propionate, and this reaction has been confirmed in humans and mice.
JOURNAL OF LIPID RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Marie-Line Bortolin-Cavaille, Quillien Aurelie, Thalalla Gamage Supuni, Justin M. Thomas, Aldema Sas-Chen, Sunny Sharma, Celia Plisson-Chastang, Laurence Vandel, Patrick Blader, Denis L. J. Lafontaine, Schraga Schwartz, Jordan L. Meier, Jerome Cavaille
Summary: This study reveals the essential role of SNORD13 in the acetylation of a specific cytidine in human and zebrafish 18S rRNA. However, this acetylation does not have a significant impact on human cell growth, ribosome biogenesis, translation, or development. The study also identifies several novel SNORD13 genes and discovers an atypical SNORD13-like RNA in Drosophila melanogaster.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Alec G. Trub, Gregory R. Wagner, Kristin A. Anderson, Scott B. Crown, Guo-Fang Zhang, J. Will Thompson, Olga R. Ilkayeva, Robert D. Stevens, Paul A. Grimsrud, Rhushikesh A. Kulkarni, Donald S. Backos, Jordan L. Meier, Matthew D. Hirschey
Summary: Statins, commonly prescribed drugs for the prevention of cardiovascular disease, have pleiotropic effects on cells. By inhibiting HMGCR, statins increase HMG-CoA levels and modify fatty acid synthase (FAS), leading to altered cellular signaling. This study reveals communication between cholesterol and lipid biosynthesis pathways.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Christian C. Dibble, Samuel A. Barritt, Grace E. Perry, Evan C. Lien, Renee C. Geck, Sarah E. DuBois-Coyne, David Bartee, Thomas T. Zengeya, Emily B. Cohen, Min Yuan, Benjamin D. Hopkins, Jordan L. Meier, John G. Clohessy, John M. Asara, Lewis C. Cantley, Alex Toker
Summary: In response to hormones and growth factors, the PI3K signalling network plays a crucial role in regulating metabolism and growth by controlling cellular nutrient uptake, energy generation, cofactor production, and macromolecule biosynthesis. This study reveals that PI3K signalling stimulates the de novo synthesis of coenzyme A (CoA), a key metabolic cofactor, and identifies PANK2 and PANK4 as substrates of the PI3K effector kinase AKT. Furthermore, the study shows that PANK4 acts as a suppressor of CoA synthesis and phosphorylation by AKT relieves this suppression. Ultimately, the PI3K-PANK4 axis regulates important processes such as lipid metabolism and proliferation by controlling the abundance of acetyl-CoA and other acyl-CoAs.
Article
Biochemistry & Molecular Biology
Minervo Perez, Kellie D. Nance, Daniel W. Bak, Supuni Thalalla Gamage, Susana S. Najera, Amy N. Conte, W. Marston Linehan, Eranthie Weerapana, Jordan L. Meier
Summary: This study found that the electrophilicity of the metabolome in Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) may lead to unique susceptibilities to covalent small molecules, resulting in cytotoxicity. The chemoproteomic target identification method can be used to identify new functional oncometabolite targets.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Supuni Thalalla Gamage, Marie-Line Bortolin-Cavaille, Courtney Link, Keri Bryson, Aldema Sas-Chen, Schraga Schwartz, Jerome Cavaille, Jordan L. Meier
Summary: There are two methods for studying RNA-guided cytidine acetylation in human cells: rescuing h45 in a SNORD13 knockout cell line by ectopically expressing SNORD13, and defining the structure and sequence elements critical for SNORD13 function by using mutant snoRNAs in combination with nucleotide resolution ac(4)C sequencing. Additionally, the substrate specificity of endogenous NAT10-SNORD13 can be studied through mutational analysis of an ectopically expressed pre-rRNA substrate.
Meeting Abstract
Oncology
Ruhul Amin, Ngoc-Han Ha, Jordan L. Meier, Kent W. Hunter
Article
Biochemistry & Molecular Biology
Kellie D. Nance, Supuni Thalalla Gamage, Md Masud Alam, Acong Yang, Michaella J. Levy, Courtney N. Link, Laurence Florens, Michael P. Washburn, Shuo Gu, Joost J. Oppenheim, Jordan L. Meier
Summary: Synthetic mRNA is a promising therapeutic platform in oncology and infectious disease treatment. The naturally occurring nucleobase N-4-acetylcytidine (ac4C) can reduce inflammatory gene expression in immune cells caused by synthetic mRNA, thereby modulating RNA-protein interactions.
CELL CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Susanne Mueller, Suzanne Ackloo, Arij Al Chawaf, Bissan Al-Lazikani, Albert Antolin, Jonathan B. Baell, Hartmut Beck, Shaunna Beedie, Ulrich A. K. Betz, Gustavo Arruda Bezerra, Paul E. Brennan, David Brown, Peter J. Brown, Alex N. Bullock, Adrian J. Carter, Apirat Chaikuad, Mathilde Chaineau, Alessio Ciulli, Ian Collins, Jan Dreher, David Drewry, Kristina Edfeldt, Aled M. Edwards, Ursula Egner, Stephen Frye, Stephen M. Fuchs, Matthew D. Hall, Ingo Hartung, Alexander Hillisch, Stephen H. Hitchcock, Evert Homan, Natarajan Kannan, James R. Kiefer, Stefan Knapp, Milka Kostic, Stefan Kubicek, Andrew R. Leach, Sven Lindemann, Brian D. Marsden, Hisanori Matsui, Jordan L. Meier, Daniel Merk, Maurice Michel, Maxwell R. Morgan, Anke Mueller-Fahrnow, Dafydd R. Owen, Benjamin G. Perry, Saul H. Rosenberg, Kumar Singh Saikatendu, Matthieu Schapira, Cora Scholten, Sujata Sharma, Anton Simeonov, Michael Sundstrom, Giulio Superti-Furga, Matthew H. Todd, Claudia Tredup, Masoud Vedadi, Frank von Delft, Timothy M. Willson, Georg E. Winter, Paul Workman, Cheryl H. Arrowsmith
Summary: Twenty years after the first draft of the human genome was published, our understanding of the human proteome is still incomplete. The majority of proteins in the human proteome remain uncharacterized, with only a small percentage successfully targeted for drug discovery. Target 2035 aims to bridge this gap by developing new technologies for the entire human proteome by 2035.
RSC MEDICINAL CHEMISTRY
(2022)