Article
Multidisciplinary Sciences
Nejc Kejzar, Elina Laanto, Ilona Rissanen, Vahid Abrishami, Muniyandi Selvaraj, Sylvain Moineau, Janne Ravantti, Lotta-Riina Sundberg, Juha T. Huiskonen
Summary: This study characterizes the Phi CjT23 bacteriophage, which infects Flavobacterium sp. and has similarities to dsDNA viruses in the Bamfordvirae kingdom. The minimalistic structure of Phi CjT23 serves as a model for the last common ancestor between ssDNA and dsDNA viruses. Additionally, Phi CjT23 and the related phage FLiP have a global distribution and a shared evolutionary origin.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Francesco Salini, Lucilla Iacumin, Giuseppe Comi, Leon M. T. Dicks
Summary: Bacteriocins are proteinaceous toxins produced by bacteria and archaea, which have antimicrobial activity against closely related species. In this study, a new bacteriocin gene cluster was discovered, providing insights into understanding the production mechanism of thermophilin 13.
Article
Biochemistry & Molecular Biology
Guo Liu, Zhihua Wu, Yan Peng, Xiuhua Shang, Liqiong Gao
Summary: In this study, the transcriptome and proteome profiles of Plukenetia volubilis seeds at two developmental stages were analyzed. The analysis identified unique differentially expressed genes and abundant proteins at different stages of seed development. Additionally, the physicochemical properties and expression patterns of ribosome-inactivating proteins (RIPs) in different organs of P. volubilis were comprehensively analyzed. This study provides valuable evidence for the safety of oil production from P. volubilis and lays a theoretical foundation for further research and utilization of RIPs in this plant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Yan Wang, Peng Wang, Hai-Yan Cao, Hai-Tao Ding, Hai-Nan Su, Shi-Cheng Liu, Guangfeng Liu, Xia Zhang, Chun-Yang Li, Ming Peng, Fuchuan Li, Shengying Li, Yin Chen, Xiu-Lan Chen, Yu-Zhong Zhang
Summary: This study reports the structure and collagenolytic mechanism of Vibrio collagenase VhaC, providing new insights into bacterial collagenolysis.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Fernanda Cornejo-Granados, Thomas A. Kohl, Flor Vasquez Sotomayor, Sonke Andres, Rogelio Hernandez-Pando, Juan Manuel Hurtado-Ramirez, Christian Utpatel, Stefan Niemann, Florian P. Maurer, Adrian Ochoa-Leyva
Summary: This study represents the first systematic prediction and in silico characterization of the MAB secretome. Bioinformatics strategies can help to broadly explore mycobacterial secretomes, including those of clinical isolates, and tailor subsequent experimental approaches accordingly. The approach can support systematic investigation exploring candidate proteins for new vaccines and diagnostic markers to distinguish between colonization and infection.
Article
Biochemistry & Molecular Biology
Dominique A. Doyle, Florencia N. Burian, Benjamin Aharoni, Annabelle J. Klinder, Melissa M. Menzel, Gerard Carlo C. Nifras, Ahad L. Shabazz-Henry, Bianca Ulrich Palma, Gisselle A. Hidalgo, Christopher J. Sottolano, Bianca M. Ortega, Matthew G. Niepielko
Summary: mRNA packaging into germ granules is a conserved strategy for posttranscriptional regulation of germline mRNAs. We studied the homotypic clustering of nos and pgc in four Drosophila species and found that clustering is a conserved process that enriches germ granule mRNAs. Natural variations in nos 3ʹ UTR sequence influence clustering, resulting in decreased nos levels and increased defective germ cells. Our findings highlight the impact of evolution on germ granules and provide insight into the diversity and regulation of biomolecular condensates.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
News Item
Medicine, General & Internal
Revital Marcus
Summary: This Medical News article explores the potential link between hormonal fluctuations, calcitonin gene-related peptide (CGRP), and migraines in women.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Biochemistry & Molecular Biology
Christina Ferousi, Christos Kosinas, Efstratios Nikolaivits, Evangelos Topakas, Maria Dimarogona
Summary: In this study, the crystal structure of a Feruloyl esterase (FoFaeC) from Fusarium oxysporum in complex with p-coumaric acid was reported, providing the first ligand-bound structure of a tannase-like Feruloyl esterase. The data showed local conformational changes around the active site upon ligand binding, suggesting interconversion between an active and a resting state of the enzyme. A swinging tyrosine residue was found to gate the substrate binding pocket, while the lid domain of the protein exerted substrate specificity through a well-defined hydrophobic core that encased the phenyl moiety of the substrate.
Article
Oncology
Felicity Newell, Peter A. Johansson, James S. Wilmott, Katia Nones, Vanessa Lakis, Antonia L. Pritchard, Serigne N. Lo, Robert Rawson, Stephen H. Kazakoff, Andrew J. Colebatch, Lambros T. Koufariotis, Peter M. Ferguson, Scott Wood, Conrad Leonard, Matthew H. Law, Kelly M. Brooks, Natasa Broit, Jane M. Palmer, Kasey L. Couts, Ismael A. Vergara, Georgina Long, Andrew P. Barbour, Omgo E. Nieweg, Brindha Shivalingam, William A. Robinson, Jonathan R. Stretch, Andrew J. Spillane, Robyn P. M. Saw, Kerwin F. Shannon, John F. Thompson, Graham J. Mann, John Pearson, Richard A. Scolyer, Nicola Waddell, Nicholas K. Hayward
Summary: This is the largest whole-genome analysis of melanoma to date, comprehensively comparing the genomics of the four major melanoma subtypes. This study highlights both similarities and differences between the subtypes, providing insights into the etiology and biology of melanoma.
Article
Multidisciplinary Sciences
Jianxiang Ma, Pengchuan Sun, Dandan Wang, Zhenyue Wang, Jiao Yang, Ying Li, Wenjie Mu, Renping Xu, Ying Wu, Congcong Dong, Nawal Shrestha, Jianquan Liu, Yongzhi Yang
Summary: The study reports the high-quality genome of Chloranthus sessilifolius, revealing the genome duplication within the species and the phylogenetic relationships with other Mesangiospermae lineages. Additionally, the findings suggest that both hybridization and incomplete lineage sorting may have contributed to the phylogenetic incongruities.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Katie Leap, Iveta Yotova, Steve Horvath, Julian A. Martinez-Agosto
Summary: Endometriosis is a common disease with various presentations. The use of DNA methylation age can help distinguish the origin of ectopic lesions, contributing to clinical classification.
SCIENTIFIC REPORTS
(2022)
Article
Ophthalmology
Wilson Luu, Barbara Zangerl, Michael Kalloniatis, Stephen Palmisano, Juno Kim
Summary: This study found that participants with AMD exhibited stronger vection and spatial presence in self-motion perception, while individuals with glaucoma showed lower vection strength and spatial presence. Both AMD and glaucoma groups reported reduced severity in cybersickness compared to healthy normals.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Francesca A. Vaccaro, David A. Born, Catherine L. Drennan
Summary: G-protein metallochaperone MeaB facilitates the delivery of AdoCbl to MCM and genetic defects in MMAA lead to methylmalonic aciduria. The crystal structure of MeaB bound to a GTP analog GMPPCP with the Cbl-binding domain of MeMCMcbl reveals the activation mechanism of MeaB by target protein binding and the rearrangement of switch III region. These results provide insights into the molecular basis of AdoCbl delivery and the role of GTP hydrolysis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Engineering, Biomedical
Abba E. Coron, Davi M. Fonseca, Animesh Sharma, Geir Slupphaug, Berit L. Strand, Anne Mari A. Rokstad
Summary: This study investigated the protein adsorption profiles of alginate hydrogel microspheres and evaluated their biological significance using mass spectrometry-based proteomics. Different microspheres exhibited distinct inflammatory and fibrotic responses. Proteomic profiling revealed complement and coagulation as the top enriched pathways, indicating the potential role of these pathways in host response.
MATERIALS TODAY BIO
(2022)
Article
Plant Sciences
Joon Hyuk Suh, Xixuan Tang, Yi Zhang, Frederick G. Gmitter, Yu Wang
Summary: This study used a multiple pathway-targeted metabolomic approach to elucidate the metabolic mechanisms of HLB tolerance in citrus. The findings revealed a pivotal metabolic network associated with HLB tolerance, showing that pathways linked to plant growth, phloem regeneration, and energy-yielding metabolism were upregulated in HLB-tolerant cultivars. Additionally, metabolites related to plant defense responses were decreased in the tolerant group, indicating a strategy of sustaining plant growth and phloem formation rather than direct plant defense against the disease.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Hehua Liu, Rui Wang, Xiang Yu, Fusheng Shen, Wenxian Lan, Phensinee Haruehanroengra, Qingqing Yao, Jing Zhang, Yiqing Chen, Suhua Li, Baixing Wu, Lina Zheng, Jinbiao Ma, Jinzhong Lin, Chunyang Cao, Jixi Li, Jia Sheng, Jianhua Gan
NUCLEIC ACIDS RESEARCH
(2018)
Article
Cell Biology
Ting Shen, Huan Li, Yifang Song, Li Li, Jinzhong Lin, Gang Wei, Ting Ni
Article
Biochemistry & Molecular Biology
Xin Wang, Zhi-Tong Li, Yue Yan, Penghui Lin, Wei Tang, Daniele Hasler, Rajyalakshmi Meduri, Ye Li, Min-Min Hua, Hui-Tao Qi, Di-Hang Lin, Hui-Juan Shi, Jingyi Hui, Jinsong Li, Dangsheng Li, Jian-Hua Yang, Jinzhong Lin, Gunter Meister, Utz Fischer, Mo-Fang Liu
Article
Biochemistry & Molecular Biology
Dejian Zhou, Takehito Tanzawa, Jinzhong Lin, Matthieu G. Gagnon
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Ru-Juan Liu, Tao Long, Hao Li, JingHua Zhao, Jing Li, MingZhu Wang, Andres Palencia, JinZhong Lin, Stephen Cusack, En-Duo Wang
NUCLEIC ACIDS RESEARCH
(2020)
Article
Chemistry, Medicinal
Weijia Li, Li Li, Chao Zhang, Yuanheng Cai, Qiyu Gao, Fulin Wang, Yu Cao, Jinzhong Lin, Jie Li, Zhuo Shang, Wei Lin
ACS INFECTIOUS DISEASES
(2020)
Article
Cell Biology
Kuanxing Gao, Man Cheng, Xinxin Zuo, Jinzhong Lin, Kurt Hoogewijs, Michael P. Murphy, Xiang-Dong Fu, Xiaorong Zhang
Summary: RNA interference (RNAi) is a gene-silencing pathway in most eukaryotic cells to protect the genome from retrotransposition. Recent studies show that transfected siRNAs can enter mitochondria and function there to specifically silence targeted mitochondrial transcripts, providing a new tool to study mitochondrial biology.
Letter
Cell Biology
Jing Lu, Guoliang Lu, Shudan Tan, Jia Xia, Hualong Xiong, Xiaofei Yu, Qingqing Qi, Xiang Yu, Li Li, Hang Yu, Ningshao Xia, Tianying Zhang, Yingjie Xu, Jinzhong Lin
Article
Cell Biology
Yingying Zhao, Liangguo Xie, Chao Shen, Qian Qi, Yicai Qin, Juan Xing, Dejian Zhou, Yun Qi, Zhiqiang Yan, Xinhua Lin, Rongyang Dai, Jinzhong Lin, Wei Yu
Summary: Mutations in GARS affect the deacetylation activity of SIRT2 on alpha-tubulin, leading to CMT neuropathies, while reducing SIRT2 can rescue the disease and extend lifespan.
Article
Multidisciplinary Sciences
Xiaofeng Chu, Xin Su, Mingdong Liu, Li Li, Tianhao Li, Yicheng Qin, Guoliang Lu, Lei Qi, Yunhui Liu, Jinzhong Lin, Qing-Tao Shen
Summary: This study investigates the effect of annealing on biological macromolecules using the 70S ribosome as a model. Experimental results show that annealing with a fast cooling rate can enhance the homogeneity and resolution of the ribosome, reaching a minimum energy state in the free-energy landscape. This approach has potential applications in improving protein stability and synchronizing proteins on a single-molecule level.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Pharmacology & Pharmacy
Wei Wang, Shuo Feng, Zhuyifan Ye, Hanlu Gao, Jinzhong Lin, Defang Ouyang
Summary: The study utilized machine learning algorithms and molecular dynamic modeling to accelerate the development of mRNA vaccine LNPs, demonstrating the feasibility of the predictive model. Experimental validation confirmed the accuracy of the predictive model, providing a new approach for virtual screening of LNP formulations in the future.
ACTA PHARMACEUTICA SINICA B
(2022)
Article
Multidisciplinary Sciences
Yangyang Li, Shichen Su, Yanqing Gao, Guoliang Lu, Hehua Liu, Xi Chen, Zhiwei Shao, Yixi Zhang, Qiyuan Shao, Xin Zhao, Jie Yang, Chulei Cao, Jinzhong Lin, Jinbiao Ma, Jianhua Gan
Summary: In this study, the crystal structure of HARP proteins and their mechanism of pre-tRNA binding and cleavage were elucidated. The results showed that HARP proteins can undergo conformational changes to facilitate pre-tRNA binding and catalytic site formation, and can assemble into larger oligomers. The study also revealed a cooperative pre-tRNA processing mode, where one HARP dimer binds pre-tRNA at the elbow region and 5'-end removal is catalyzed by the partner dimer.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Yan Liu, Zihan Wu, Damu Wu, Ning Gao, Jinzhong Lin
Summary: A Ribozyme-Assisted Polycistronic co-expression system (pRAP) was developed for heterologous co-production and in vivo assembly of multi-subunit complexes. The system allows balanced expression of subunits, allowing faithful protein complex assembly. Successful reconstitution of large functional multi-subunit complexes validates the utility of pRAP for studying biological processes.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Damu Wu, Yan Liu, Yuhao Dai, Guopeng Wang, Guoliang Lu, Yan Chen, Ningning Li, Jinzhong Lin, Ning Gao, Richard Hodge
Summary: The human AAA+ ATPase CLPB is a protein disaggregase in the mitochondrial intermembrane space and plays a role in promoting the solubilization of mitochondrial proteins. Structural characterization reveals that CLPB forms different oligomers depending on its state and contains an ANK domain essential for its disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with various mitochondrial substrates. These findings highlight the unique properties of CLPB and its potential as a therapeutic target for mitochondria-related diseases.
Article
Biochemistry & Molecular Biology
Zhaoli Yu, Zihan Wu, Ye Li, Qiang Hao, Xiaofeng Cao, Gregor M. Blaha, Jinzhong Lin, Guoliang Lu
Summary: Two types of glycyl-tRNA synthetase (GlyRS) have been identified, alpha(2) and alpha(2)beta(2) GlyRSs. While the mechanisms for alpha(2) GlyRSs are well understood, little is known about the mechanisms for alpha(2)beta(2)/(alpha beta)(2) GlyRSs. This study presents the structures of the (alpha beta)(2) GlyRS from Oryza sativa chloroplast, revealing a complex mechanism of tRNA selection and access to the active site.
NUCLEIC ACIDS RESEARCH
(2023)