Article
Plant Sciences
Chuyu Lin, Zhongling Wu, Huanbin Shi, Jinwei Yu, Mengting Xu, Fucheng Lin, Yanjun Kou, Zeng Tao
Summary: This study reveals the critical role of an additional subunit of PRC2, P55, in the normal distribution of H3K27me3 and the stable maintenance of gene repression in the rice fungal pathogen Magnaporthe oryzae. Loss of P55 leads to severe defects in the distribution of H3K27me3 and transcriptional reprogramming. It was also discovered that the Sin3 histone deacetylase complex plays a crucial role in sustaining H3K27me3 occupancy and gene repression by interacting with P55.
Article
Medicine, Research & Experimental
Lei Bao, Ashwani Kumar, Ming Zhu, Yan Peng, Chao Xing, Jennifer E. Wang, Yingfei Wang, Weibo Luo
Summary: SAP30 is an important protein in breast cancer, and its upregulation is associated with unfavorable prognosis. Research has shown that SAP30 promotes tumor growth and metastasis through mechanisms other than canonical gene silencing. Additionally, SAP30 enhances cell motility, angiogenesis, and lymphangiogenesis by interacting with other proteins, thereby driving breast cancer progression.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Engineering, Biomedical
Xinman Song, Kazuto Okabe, Yuya Ohta, Go Ohara, Naoto Toyama, Qi Chang, Yilin Wang, Hideharu Hibi
Summary: FAM20B plays a crucial role in osteogenic differentiation and bone formation on titanium surfaces. Depletion of FAM20B inhibits the formation of a PG-rich layer between bone cells and titanium surfaces, reduces MSC osteogenesis signaling pathway, and decreases the expression of osteogenic marker genes.
ACTA BIOMATERIALIA
(2023)
Article
Biochemistry & Molecular Biology
Zhouyan Guo, Chen Chu, Yichen Lu, Xiaofeng Zhang, Yihang Xiao, Mingxuan Wu, Shuaixin Gao, Catherine C. L. Wong, Xiechao Zhan, Chengcheng Wang
Summary: This study presents the cryo-EM structure of the yeast SIN3-HDAC complex Rpd3L, revealing a distinctive organization mechanism compared with other class I HDAC complexes. The structure shows two distinct arms that interact with different subunits, resulting in an asymmetric architecture of Rpd3L.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Gastroenterology & Hepatology
Yi-Xin Guo, Bing Han, Ting Yang, Yu-Si Chen, Yi Yang, Jia-Yao Li, Qin Yang, Ru-Jia Xie
Summary: This study elucidates the effect of FAM134B-mediated endoplasmic reticulum (ER)-phagy on ER stress-induced apoptosis in rat hepatocytes and investigates the potential regulatory mechanisms. The findings suggest that FAM134B-mediated ER-phagy attenuates hepatocyte apoptosis by suppressing the mitochondrial apoptotic pathway.
WORLD JOURNAL OF GASTROENTEROLOGY
(2022)
Article
Multidisciplinary Sciences
Aidan L. Huene, Steven M. Sanders, Zhiwei Ma, Anh-Dao Nguyen, Sergey Koren, Manuel H. Michaca, James C. Mullikin, Adam M. Phillippy, Christine E. Schnitzler, Andreas D. Baxevanis, Matthew L. Nicotra
Summary: Most colonial marine invertebrates have the ability to distinguish between themselves and conspecifics, known as allorecognition. In the cnidarian Hydractinia symbiolongicarpus, allorecognition is controlled by at least two genes, Allorecognition 1 (Alr1) and Allorecognition 2 (Alr2), which encode highly polymorphic cell-surface proteins. These proteins are members of the immunoglobulin superfamily (IgSF), with V-set and I-set Ig domains unlike any previously identified in animals. The discovery of these genes expands our understanding of invertebrate histocompatibility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Christopher M. Hoel, Lin Zhang, Stephen G. Brohawn
Summary: TMEM87s are a family of transmembrane proteins found in humans, which play important roles in protein transport, mechanosensitive ion channel activity, and developmental signaling. This study focuses on the structure and function of TMEM87A, and reveals its similarities with other structurally homologous proteins. The findings suggest that TMEM87A may have a common role in trafficking membrane-associated cargo, similar to WLS.
Article
Multidisciplinary Sciences
Mercedes Spinola-Amilibia, Lidia Araujo-Bazan, Alvaro de la Gandara, James M. Berger, Ernesto Arias-Palomo
Summary: Transposases are enzymes that play a role in DNA rearrangement and have broad impacts on gene expression, genome evolution, and the spread of drug-resistance in bacteria. This study investigates the molecular determinants of IstA, a transposase in the IS21 family, and reveals its structure and mechanism of action in DNA transposition. The research findings provide new insights into IS21 transposition.
NATURE COMMUNICATIONS
(2023)
Article
Fisheries
Yi Gong, Fei Wu, Haoyi Li, Xiangmin Zhang, Shicui Zhang
Summary: AP2M1A is a heparin-binding protein that exhibits resistance to oxidative damage and antibacterial activity. It interacts with LPS and LTA to disrupt bacterial cell walls, disturb membranes, and induce apoptosis/necrosis. Research also found that AP2M1A can protect zebrafish larvae from Aeromonas hydrophila infection.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Juan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Melendez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones
Summary: Studying the evolutionary history of gene families is important for understanding gene origin, evolution, and their implications for functional studies. The sirtuin gene family, involved in aging-related functions, has a complex duplicative history, but our results provide a well-resolved phylogeny and shed light on the repertoire of sirtuin genes among vertebrates. We identified a new member (SIRT3.2) that was lost in amniotes but retained in other jawed vertebrates, and its experimental analysis revealed its mitochondrial location and deacetylase activity similar to mammalian SIRT3.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Md. Mikail Hossain, Sultana Rajia, Mayuka Ohkawa, Suzuna Yoshimoto, Yuki Fujii, Sarkar M. A. Kawsar, Yasuhiro Ozeki, Imtiaj Hasan
Summary: MytiLec-1, a recombinant mussel lectin from Mytillus galloprovincialis, has been found to have antimicrobial activity by inhibiting the growth of Pseudomonas aeruginosa and preventing the formation of biofilms. It is also able to agglutinate the spores of Aspergillus niger and Trichoderma reesei. The study compares the amino acid sequences, physicochemical properties, and antimicrobial activities of MytiLec-1 with other lectins from bivalve mollusks, reaffirming the importance of lectins in the innate immune response of mussels.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemical Research Methods
Anna Klimovskaia Susmelj, Yani Ren, Yann Vander Meersche, Jean-Christophe Gelly, Tatiana Galochkina
Summary: In the era of increasing protein data, a relevant and interpretable visualization is crucial. Poincare disk projection has shown its efficiency in visualizing single-cell RNAseq data. Here, we introduce PoincareMSA, a new method for visualizing complex relationships between protein sequences using Poincare maps embedding. It demonstrates efficiency in visualizing protein family topology and annotating unknown sequences. PoincareMSA is implemented in open source Python code with available interactive Google Colab notebooks.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Plant Sciences
Xia Chen, Barbara Lesniewska, Rodion Boikine, Nicole Yun, Tejasvinee Atul Mody, Prasad Vaddepalli, Kay Schneitz
Summary: Intercellular communication is crucial for organogenesis. The study investigates the architecture and maintenance of the QKY/SUB signaling complex and its role in tissue morphogenesis using genetics and microscopy techniques. They found that QKY promotes the formation of SUB homooligomers and physically interacts with SUB at the cell surface. The interaction between QKY and SUB is essential for maintaining SUB levels and controlling tissue morphogenesis.
Article
Microbiology
Shan Jiang, Feng-Bai Lian, You-Yang Sun, Xiao-Kui Zhang, Zong- Jun Du
Summary: The bacterial strain F7430(T) isolated from coastal sediment in Weihai, PR China, was identified as a novel species within the family Halieaceae, named Sediminihaliea albiluteola gen. nov., sp. nov. The strain exhibited unique physiological and genetic characteristics, distinguishing it as a new species within this family.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Review
Immunology
Jie-Jie Xu, Hai-Di Li, Xiao-Sa Du, Juan-Juan Li, Xiao-Ming Meng, Cheng Huang, Jun Li
Summary: PSTPIP2, a member of the F-BAR domain family, plays important roles in immune and inflammatory processes, making it a potential therapeutic target for AIDs. While it has been found that proteins like PTP-PEST, SHIP1, and CSK can bind to PSTPIP2 and inhibit AIDs development, the exact mechanisms of PSTPIP2's function remain to be fully elucidated.
FRONTIERS IN IMMUNOLOGY
(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
Virology
Peter J. Walker, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Andrew J. Davison, Donald M. Dempsey, Bas E. Dutilh, Maria Laura Garcia, Balazs Harrach, Robert L. Harrison, R. Curtis Hendrickson, Sandra Junglen, Nick J. Knowles, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Max L. Nibert, Hanna M. Oksanen, Richard J. Orton, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Nobuhiro Suzuki, Koenraad Van Dooerslaer, Anne-Mieke Vandamme, Arvind Varsani, Francisco Murilo Zerbini
Summary: This article reports the changes to virus taxonomy approved and ratified by ICTV in March 2021. All proposals and revisions were passed by an absolute majority of ICTV members. ICTV mandated a new uniform rule for virus species naming, abolished the notion of a type species, and clarified its remit through an official definition of 'virus' and other types of mobile genetic elements.
ARCHIVES OF VIROLOGY
(2021)
Article
Multidisciplinary Sciences
Soon-Keat Ooi, Shigeo Sato, Chieri Tomomori-Sato, Ying Zhang, Zhihui Wen, Charles A. S. Banks, Michael P. Washburn, Jay R. Unruh, Laurence Florens, Ronald C. Conaway, Joan W. Conaway
Summary: PARP1 has multiple functions in ALC1-dependent nucleosome remodeling beyond simply synthesizing PAR chains, as shown by investigation of separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Francisco Murilo Zerbini, Stuart G. Siddell, Arcady R. Mushegian, Peter J. Walker, Elliot J. Lefkowitz, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Bas E. Dutilh, Maria Laura Garcia, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani
Summary: Following the ICTV Ratification Vote in March 2021, a standard two-part binomial nomenclature is now the standard for naming virus species. The adoption of this new nomenclature is still in its early stages, making it timely to clarify the distinction between viruses and virus species and provide guidelines for their correct naming and writing.
ARCHIVES OF VIROLOGY
(2022)
Review
Plant Sciences
Olga Tsoy, Arcady Mushegian
Summary: This article mainly introduces the research on the product of the FT gene as a key component of florigen, and discusses the molecular features and functions of FT homologs, suggesting that they may act as enzymes on small molecule metabolites.
Review
Biochemistry & Molecular Biology
Irina Sorokina, Arcady R. Mushegian, Eugene V. Koonin
Summary: The prevailing thermodynamic hypothesis of protein folding is called into question due to the lack of strong empirical evidence. Physical theory-based approaches in predicting protein folds have largely failed, except for small proteins. Recent successes in protein structure prediction have been achieved through evolutionary modeling and deep learning methods, but provide no insights into protein folding mechanisms and pathways. An alternative view suggests that most proteins do not occupy the global minimum of free energy, but instead a local minimum on a fluctuating landscape. This view also argues that the majority of proteins require energy-dependent cellular processes for folding, such as interactions with the translation system and chaperones.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Rosalyn C. Zimmermann, Mihaela E. Sardiu, Christa A. Manton, Md. Sayem Miah, Charles A. S. Banks, Mark K. Adams, Devin C. Koestler, Douglas R. Hurst, Mick D. Edmonds, Michael P. Washburn, Danny R. Welch
Summary: The C-terminus of BRMS1 plays a critical role in metastasis suppression, with its phosphorylation status affecting protein interactions related to various biological processes and metastasis. These findings significantly contribute to understanding how BRMS1 regulates metastasis through interactions with Sin3/HDAC complexes and expand insights into the molecular role of BRMS1.
Article
Multidisciplinary Sciences
Saikat Bhattacharya, Suman Wang, Divya Reddy, Siyuan Shen, Ying Zhang, Ning Zhang, Hua Li, Michael P. Washburn, Laurence Florens, Yunyu Shi, Jerry L. Workman, Fudong Li
Summary: The paper describes the interaction between hnRNP L and SETD2, revealing their binding mechanism. The study demonstrates that a leucine pair in SETD2 inserts their side chains in hydrophobic pockets formed by hnRNP L RRM2 for interaction to occur, highlighting the importance of this binding interaction. The similarity in the mode of SETD2-hnRNP L interaction with other related protein-protein interactions suggests a conserved design for splicing regulators to interact with one another.
NATURE COMMUNICATIONS
(2021)
Article
Virology
Peter J. Walker, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Donald M. Dempsey, Bas E. Dutilh, Maria Laura Garcia, R. Curtis Hendrickson, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, Richard J. Orton, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, Francisco Murilo Zerbini
Summary: This article discusses the changes in virus taxonomy approved by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The ICTV members voted on 174 taxonomic proposals, all of which were ratified by an absolute majority. The implementation of a new naming rule for virus species has resulted in over 60% of virus species being named in the 'Genus_name species_epithet' format.
ARCHIVES OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Arcady Mushegian
Summary: Methyltransferases play an important role in the interaction between viruses and eukaryotic hosts. In Riboviria, these methyltransferases have structural similarities to the widespread FtsJ/RrmJ-like methyltransferases in cells, but there are also different classes of methyltransferases. Analysis of spatial structures revealed that conserved residues play a crucial role in the catalytic mechanism. Phylogenetic evidence suggests that methyltransferases in Riboviria likely originated from cellular RrmJ-like enzymes and have undergone rapid divergence with infrequent horizontal transfer between different viruses.
Article
Virology
Francisco Murilo Zerbini, Stuart G. Siddell, Elliot J. Lefkowitz, Arcady R. Mushegian, Evelien M. Adriaenssens, Poliane Alfenas-Zerbini, Donald M. Dempsey, Bas E. Dutilh, Maria Laura Garcia, R. Curtis Hendrickson, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Malgorzata Lobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Smith, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani
Summary: This article reports on changes to virus taxonomy and nomenclature approved by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. All ICTV members were invited to vote on 174 taxonomic proposals and a revision of the ICTV Statutes that had been approved by the ICTV Executive Committee in July 2022. Majority approval was obtained for all proposals and the revised ICTV Statutes. A significant change was the renaming of existing species according to the binomial format and the classification of gene transfer agents (GTAs) as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.
ARCHIVES OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Harutyun Sahakyan, Karen Nazaryan, Arcady Mushegian, Irina Sorokina
Summary: Molecular dynamics simulations were performed to study protein folding. By applying rotational force to the C-terminal amino acid while restricting the movement of the N-terminal amino acid, the folding of four protein domains was accelerated at least by an order of magnitude. These results suggest that external forces and constraints can bias the motions of the polypeptide and facilitate the attainment of stable fold.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Colin S. McCoin, Edziu Franczak, Michael P. Washburn, Mihaela E. Sardiu, John P. Thyfault
Summary: The study utilized proteomics to analyze the effects of exercise on the mitochondrial proteome in female mice, revealing rapid changes in mitochondrial protein/pathways with acute exercise, including fatty acid metabolism/storage, post-translational protein modification, inflammation, and oxidative stress.
Article
Developmental Biology
Narendra Pratap Singh, Bony De Kumar, Ariel Paulson, Mark E. Parrish, Carrie Scott, Ying Zhang, Laurence Florens, Robb Krumlauf
Summary: The study revealed that the majority of HOXB1 binding regions in mouse embryonic stem cells differentiated into neural fates do not correlate with known HOX cofactors, but display significant co-occupancy with the transcriptional repressor REST. Furthermore, a novel 15 base pair HOXB1 binding motif, HB1RE, was identified in HOXB1 bound regions, contributing to its repressive function in gene expression.
JOURNAL OF DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mihaela E. Sardiu, Andrew C. Box, Jeffrey S. Haug, Michael P. Washburn
Summary: Machine learning and topological analysis methods are increasingly utilized for large-scale omics datasets, including flow cytometry data which shares similarities with genomics and proteomics datasets. The TopS approach has been shown to effectively analyze flow cytometry datasets, identifying rare cell populations and providing novel insights into the data patterns. Coupling TopS with various methods like topological data analysis, X-shift clustering, and t-SNE can further enhance the analysis of large-scale flow cytometry datasets.
