Article
Biochemistry & Molecular Biology
Dario Monachello, Marc Lauraine, Sandra Gillot, Francois Michel, Maria Costa
Summary: Mobile group II introns are retrotransposable elements that insert themselves into DNA target sites with the help of base-pairing interactions and the reverse transcriptase enzyme. A new base-pairing interaction named EBS2a-IBS2a has been identified, which is crucial for intron mobility by driving unwinding of the DNA duplex and is stabilized by the reverse transcriptase in a non-sequence-specific manner. This discovery has important implications for the biotechnological applications of group II introns in bacterial gene targeting.
NUCLEIC ACIDS RESEARCH
(2021)
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
Plant Sciences
Leila Feiz, Yukari Asakura, Linyong Mao, Susan R. Strickler, Zhangjun Fei, Margarita Rojas, Alice Barkan, David B. Stern
Summary: A new study shows that CRM Family Member1 (CFM1) facilitates the splicing of chloroplast introns in plants, particularly those not previously known to require CRM domain proteins. Deficiencies in these introns result in compromised chloroplast protein synthesis, leading to whole-plant chlorotic phenotypes.
Article
Multidisciplinary Sciences
Anjie Xia, Xihao Yong, Changbin Zhang, Guifeng Lin, Guowen Jia, Chang Zhao, Xin Wang, Yize Hao, Yifei Wang, Pei Zhou, Xin Yang, Yue Deng, Chao Wu, Yujiao Chen, Jiawei Zhu, Xiaodi Tang, Jingming Liu, Shiyu Zhang, Jiahao Zhang, Zheng Xu, Qian Hu, Jinlong Zhao, Yuting Yue, Wei Yan, Zhaoming Su, Yuquan Wei, Rongbin Zhou, Haohao Dong, Zhenhua Shao, Shengyong Yang
Summary: This study presents the cryo-EM structures of GPR34 bound with LysoPS and its inhibition by the antagonist YL-365. The findings provide mechanistic insights into the endogenous agonist recognition and antagonist inhibition of GPR34, highlighting GPR34 as a promising target for disease treatment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Genetics & Heredity
Ron Mizrahi, Sofia Shevtsov-Tal, Oren Ostersetzer-Biran
Summary: Mitochondria are organelles responsible for cellular energy production. Plant mitochondria have introns that play a significant role in protein splicing. These splicing processes are regulated by various protein factors and may be associated with cellular and environmental signals.
Article
Biochemical Research Methods
Chih-Chia Su, Meinan Lyu, Christopher E. Morgan, Jani Reddy Bolla, Carol V. Robinson, Edward W. Yu
Summary: The development of the Build and Retrieve (BaR) method allows for the identification and determination of cryo-EM structures of various inner and outer membrane proteins from heterogeneous protein samples, demonstrating the potential of cryo-EM in systems structural proteomics.
Article
Biochemistry & Molecular Biology
Li Zhang, Jingli Chen, Liqun Zhang, Ying Wei, Yajuan Li, Xinyun Xu, Hui Wu, Zhong-Nan Yang, Jirong Huang, Fenhong Hu, Weihua Huang, Yong-Lan Cui
Summary: The plastid-localized PPR protein EMB1270 is essential for chloroplast biogenesis in Arabidopsis thaliana, playing a crucial role in the accumulation of photosynthetic proteins and splicing efficiency of specific plastid introns. EMB1270 interacts with CFM2 to facilitate the splicing of group II introns, highlighting its importance in coordinating chloroplast and nuclear gene expression.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Clinical Neurology
Grace Hallinan, Kadir A. Ozcan, Md Rejaul Hoq, Laura Cracco, Frank S. Vago, Sakshibeedu R. Bharath, Daoyi Li, Max Jacobsen, Emma H. Doud, Amber L. Mosley, Anllely Fernandez, Holly J. Garringer, Wen Jiang, Bernardino Ghetti, Ruben Vidal
Summary: The aggregation of Prion protein (PrP) and formation of PrP amyloid (APrP) are crucial events in the development of prion diseases. Gerstmann-Straussler-Scheinker (GSS) disease, a dominantly inherited form of prion protein amyloidosis, is characterized by the presence of PrP amyloid plaques throughout the brain. Cryo-EM analysis of APrP filaments isolated from GSS patients with the F198S mutation revealed their complex structure, highlighting the importance of understanding filament structures in human neurodegenerative diseases.
ACTA NEUROPATHOLOGICA
(2022)
Review
Pharmacology & Pharmacy
Christian Dahlstroem, Themistoklis Paraschiakos, Han Sun, Sabine Windhorst
Summary: Cellular actin dynamics is regulated by various actin binding proteins (ABPs), including nucleating, bundling, cross-linking, capping, and severing proteins. This review focuses on the regulation of actin dynamics by ABPs, with a specific emphasis on the role of cofilin-1, an F-actin severing protein, and L-plastin, an F-actin bundling protein. As the up-regulation of these proteins in cancer is associated with malignant progression, the cryo-EM structure of F-actin with the respective ABP could be used as a template for in silico drug design to disrupt their interaction.
BIOCHEMICAL PHARMACOLOGY
(2023)
Article
Multidisciplinary Sciences
Omar De Bei, Marialaura Marchetti, Luca Ronda, Eleonora Gianquinto, Loretta Lazzarato, Dimitri Y. Chirgadze, Steven W. Hardwick, Lee R. Cooper, Francesca Spyrakis, Ben F. Luisi, Barbara Campanini, Stefano Bettati
Summary: This study determines the structures of two IsdB:Hb complexes using single-particle cryo-electron microscopy, revealing the interaction mechanism between IsdB and Hb during heme extraction and the final step of heme transfer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Zhemin Zhang, Christopher E. Morgan, Robert A. Bonomo, Edward W. Yu
Summary: The COVID-19 pandemic and the rise of antimicrobial-resistant bacterial infections have significantly impacted global health. Klebsiella pneumoniae, a Gram-negative pathogen, is a common cause of secondary bacterial infections in COVID-19 patients, with a mortality rate of 83%. The emergence of K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae, with a mortality rate of up to 71%, has raised public attention. We report the cryo-electron microscopy structures of K. pneumoniae AcrB, which plays a crucial role in drug resistance, in the absence and presence of erythromycin, providing insights into drug recognition and pump-drug interactions.
Article
Biochemistry & Molecular Biology
Xiulian Yu, Tao Ni, George Munson, Peijun Zhang, Robert J. C. Gilbert
Summary: In this study, the structure of Perforin-2 in different conformations was determined using multiple techniques. The mechanism of pore formation in acidification conditions was found to be related to the conformational transition of the pre-pores, and it was observed that PFN2 pores mainly exist as incomplete arc structures on membranes.
Article
Biochemistry & Molecular Biology
Xiulian Yu, Tao Ni, George Munson, Peijun Zhang, Robert J. C. Gilbert
Summary: This study investigated the conformational transition of PFN2 from pre-pore to pore structures. The complete pre-pore rings found in isolation could convert into pores with different conformations. On membranes, however, the assembled PFN2 pre-pores showed various degrees of completeness, while the pores were mainly incomplete arc structures. It was also found that both assemblies utilized the P2 beta-hairpin for binding to the lipid membrane surface. These findings provide insights into the molecular mechanism of PFN2 in forming pores on targeted membranes.
Article
Multidisciplinary Sciences
Radhika Malik, Robert E. Johnson, Louise Prakash, Satya Prakash, Iban Ubarretxena-Belandia, Aneel K. Aggarwal
Summary: The study investigates the structure of the DNA-Pol zeta complex and its ability to extend DNA synthesis past mismatched base pairs. The results reveal the conformational changes in the Pol zeta active site and how it responds to mismatched DNA, allowing for the proper binding and extension of nucleotides. This study provides valuable insights into the regulation of DNA synthesis in eukaryotes.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Tomoki Ueda, Kei-ichiro Nishimura, Yuka Nishiyama, Yuto Tominaga, Katsushi Miyazaki, Hiroyuki Furuta, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Alternative splicing is an important mechanism in eukaryotic cells that allows multiple proteins to be produced from a single gene. Although it is usually associated with group I self-splicing introns, limited examples of alternative splicing have been reported. This study focuses on exon-skipping splicing in genes containing two group I introns and reveals the key structural elements important for this type of splicing through pairwise engineering and biochemical characterization.
Article
Biophysics
Reginald McNulty, Giovanni Cardone, Eddie B. Gilcrease, Timothy S. Baker, Sherwood R. Casjens, John E. Johnson
BIOPHYSICAL JOURNAL
(2018)
Review
Chemistry, Multidisciplinary
Wojciech P. Galej, Navtej Toor, Andrew J. Newman, Kiyoshi Nagai
Editorial Material
Biochemistry & Molecular Biology
Anastassia Gomez, Navtej Toor
Article
Multidisciplinary Sciences
Yong Zi Tan, Sriram Aiyer, Mario Mietzsch, Joshua A. Hull, Robert McKenna, Joshua Grieger, R. Jude Samulski, Timothy S. Baker, Mavis Agbandje-McKenna, Dmitry Lyumkis
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Rui Zhu, Longfa Xu, Qingbing Zheng, Yanxiang Cui, Shaowei Li, Maozhou He, Zhichao Yin, Dongxiao Liu, Shuxuan Li, Zizhen Li, Zhenqin Chen, Hai Yu, Yuqiong Que, Che Liu, Zhibo Kong, Jun Zhang, Timothy S. Baker, Xiaodong Yan, Z. Hong Zhou, Tong Cheng, Ningshao Xia
Article
Multidisciplinary Sciences
Russell T. Chan, Jessica K. Peters, Aaron R. Robart, Timothy Wiryaman, Kanagalaghatta R. Rajashankar, Navtej Toor
NATURE COMMUNICATIONS
(2018)
Article
Chemistry, Multidisciplinary
Rohit H. Subramanian, Sarah J. Smith, Robert G. Alberstein, Jake B. Bailey, Ling Zhang, Giovanni Cardone, Lauri Suominen, Mohamed Chami, Henning Stahlberg, Timothy S. Baker, F. Akif Tezcan
ACS CENTRAL SCIENCE
(2018)
Article
Microbiology
Qingbing Zheng, Rui Zhu, Longfa Xu, Maozhou He, Xiaodong Yan, Dongxiao Liu, Zhichao Yin, Yangtao Wu, Yongchao Li, Lisheng Yang, Wangheng Hou, Shuxuan Li, Zizhen Li, Zhenqin Chen, Zhihai Li, Hai Yu, Ying Gu, Jun Zhang, Timothy S. Baker, Z. Hong Zhou, Barney S. Graham, Tong Cheng, Shaowei Li, Ningshao Xia
NATURE MICROBIOLOGY
(2019)
Article
Multidisciplinary Sciences
Eyal Golub, Rohit H. Subramanian, Julian Esselborn, Robert G. Alberstein, Jake B. Bailey, Jerika A. Chiong, Xiaodong Yan, Timothy Booth, Timothy S. Baker, F. Akif Tezcan
Article
Cell Biology
Daniel B. Haack, Navtej Toor
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2020)
Meeting Abstract
Biotechnology & Applied Microbiology
Joshua Alexander Hull, Justin Kurian, Antonette Bennett, Balasubramanian Venkatakrishnan, Mario Mietzsch, Paul Chipman, Chen Xu, Duncan Sousa, Mandy Janssen, Timothy Baker, Robert McKenna, Mavis Agbandje-McKenna