Article
Cell Biology
Tingting Gan, Yuhong Wang, Yang Liu, David G. Schatz, Jiazhi Hu
Summary: RAG1 and RAG2 form a tetramer nuclease for V(D)J recombination in lymphocytes, with RAG1 requiring interaction with RAG2 to be activated. RAG2 disrupts RAG1 aggregates, activating recombination.
Article
Cell Biology
Yang Dong, Hao Guo, Donghai Wang, Rongfu Tu, Guoliang Qing, Hudan Liu
Summary: The study reveals that Notch1 transcriptional complexes directly activate Rag1 and Rag2 genes, with a novel cis-element SPS playing an important role in T-ALL and DN cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Rupa Kumari, Urbi Roy, Sagar Desai, Namrata M. Nilavar, Annemarie Van Nieuwenhuijze, Amita Paranjape, Gudapureddy Radha, Pushpinder Bawa, Mrinal Srivastava, Mridula Nambiar, Kithiganahalli Narayanaswamy Balaji, Adrian Liston, Bibha Choudhary, Sathees C. Raghavan
Summary: The study showed that miR-29c regulates RAG1 in a B cell stage-specific manner, modulation of miR-29c levels affects V(D)J recombination efficiency in pre-B cells, and a negative correlation between miR-29c and RAG1 levels is observed in different developmental stages.
Article
Immunology
Helen A. Beilinson, Rebecca A. Glynn, Anurupa Devi Yadavalli, Jianxiong Xiao, Elizabeth Corbett, Huseyin Saribasak, Rahul Arya, Charline Miot, Anamika Bhattacharyya, Jessica M. Jones, Jagan M. R. Pongubala, Craig H. Bassing, David G. Schatz
Summary: The RAG1 N-terminal region regulates V(D)J recombination and lymphocyte development through multiple pathways, including control of the balance between short- and long-range recombination, as shown in studies with different RAG1 mutant mice.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Doris Niewolik, Klaus Schwarz
Summary: The interaction between nuclease ARTEMIS and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) plays a crucial role in the repair of DNA double strand breaks and V(D)J recombination activity. Mutations disrupting this interaction have been found to impair the function of these proteins. Small fragments capable of mediating this interaction have been identified, offering possibilities for the design of specific inhibitors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Martin Sztacho, Barbora Salovska, Jakub Cervenka, Can Balaban, Peter Hoboth, Pavel Hozak
Summary: Analysis of nuclear protein interactions with phosphoinositides reveals the role of PIP2 in regulating gene expression, RNA splicing, and cell cycle processes. The identified proteins are involved in various functions within the nucleus, with different PIP2-binding motifs influencing their localization and activity. This study provides insights into the molecular mechanism of nuclear PIP2 protein interaction and offers a methodology for further research on PIPs and other protein ligands.
Article
Microbiology
Aline Freville, Margarida Ressurreicao, Christiaan van Ooij
Summary: Malaria parasites alter the host erythrocyte by exporting proteins into it. The presence of a PEXEL motif has been used as a signature for protein export, but this study finds that some proteins remain in the parasitophorous vacuole and are not exported. This challenges the previous understanding of PEXEL and protein processing in malaria parasites.
Article
Biochemistry & Molecular Biology
Doeun Kim, Min Seo Lee, Nam Doo Kim, Sangkyu Lee, Hye Suk Lee
Summary: The misuse of poisonous mushrooms containing amatoxins can cause acute liver failure and significant mortality. This study investigated the interaction between alpha-amanitin (alpha-AMA) and proteins in human hepatocytes using molecular docking and mass spectrometry technology, and found that alpha-AMA induces hepatotoxicity through interactions with various proteins.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Biology
Magdalena L. Russell, Aisha Souquette, David M. Levine, Stefan A. Schattgen, E. Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G. Thomas, Frederick A. Matsen, Philip Bradley
Summary: The T cell receptor repertoire is influenced by genetic biases and immune exposures. This study identifies specific genetic loci associated with V(D)J recombination probabilities and reveals variations in V(D)J gene usage profiles and the major histocompatibility complex locus that affect the TCR repertoire diversity. Furthermore, variations in genes encoding the Artemis protein and the TdT protein are found to be associated with junctional nucleotide deletion and N-insertion. These findings enhance our understanding of genetically-determined TCR repertoire biases and provide insights into individual variations in immune responses.
Article
Immunology
Anastasia O. Smirnova, Anna M. Miroshnichenkova, Laima D. Belyaeva, Ilya V. Kelmanson, Yuri B. Lebedev, Ilgar Z. Mamedov, Dmitriy M. Chudakov, Alexander Y. Komkov
Summary: Diversity of T-cell receptor (TR) variable domains is generated through recombination of alpha (TRA) and beta (TRB) chains. We analyzed poorly explored partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA and detected a bimodal distribution of D-D junctions indicating two active recombination sites. These rearrangements contribute to TRB V-(D)-J combinatorial diversity and are present in human antigen-experienced memory T cells, showing their role in antigen recognition and immune response.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Walker Hoolehan, Justin C. Harris, Karla K. Rodgers
Summary: Antigen receptor diversity is crucial for adaptive immunity in jawed vertebrates. The V(D)J recombination process generates highly diverse antigen receptor repertoires. However, the molecular mechanism for the selective recombination specificity is still unknown, as many recombination signal sequences deviate from the consensus sequence.
Article
Multidisciplinary Sciences
N. Max Schabla, Patrick C. Swanson
Summary: The study highlights the crucial role of VprBP/DCAF1 in regulating RAG1 protein levels in B cells, and demonstrates that the degradation of RAG1 protein is ubiquitin-dependent. The findings suggest that V(D)J recombination utilizes a conserved and constitutively active mechanism to ensure proper turnover of RAG1 protein and restrain excessive RAG activity.
Review
Cell Biology
Jan-Michael Peters
Summary: Structural maintenance of chromosomes' complexes play a crucial role in folding genomic DNA into loops, especially in V(D)J recombination of antigen receptor genes in B and T cells. Regulating the formation and recombination of chromatin loops ensures the diversity of B-cell receptors and antibodies.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Review
Ecology
Rishi V. Shridharan, Neha Kalakuntla, Narendra Chirmule, Bhavana Tiwari
Summary: Nearly 50% of the human genome is derived from transposable elements, some of which can cause diseases when dysregulated, while others can generate new cellular functions. The adaptive immune system in jawed vertebrates is associated with Class II TEs, and the somatic rearrangement process in T and B cells is also influenced by TEs, laying the foundation for the generation of antibodies and receptors.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Nanoscience & Nanotechnology
Jinzhi Zhao, Ruijun Jian, Yuning Wang, Beibei Yang, Dan Zhao, Chengpin Shen, Liang Qiao, Baohong Liu
Summary: A enzymatic nanoreactor using methylated well-ordered hexagonal mesoporous silica (Met-SBA-15) is designed for the digestion of membrane proteins, showing efficient extraction and digestion of hydrophobic membrane proteins from Escherichia coli and a mixed bacterial sample. This nanoreactor identifies a higher number of membrane proteins compared to traditional in-solution digestion protocols, suggesting its potential as a tool for microbial membrane proteome research in human microbiota studies.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Genetics & Heredity
William Rodgers, Jennifer N. Byrum, Hem Sapkota, Negar S. Rahman, Robert C. Cail, Shuying Zhao, David G. Schatz, Karla K. Rodgers
Article
Chemistry, Multidisciplinary
Shanjana Awasthi, Asokan Anbanandam, Karla K. Rodgers
Article
Biochemistry & Molecular Biology
Xi-Qin Ding, Arjun Thapa, Hongwei Ma, Jianhua Xu, Michael H. Elliott, Karla K. Rodgers, Marci L. Smith, Jin-Shan Wang, Steven J. Pittler, Vladimir J. Kefalov
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Review
Biochemistry & Molecular Biology
Karla K. Rodgers
TRENDS IN BIOCHEMICAL SCIENCES
(2017)
Article
Biochemistry & Molecular Biology
Olga Nikolaeva, Gennadiy Moiseyev, Karla K. Rodgers, Jian-xing Ma
BIOCHEMICAL JOURNAL
(2011)
Article
Biochemistry & Molecular Biology
M. Osman Sheikh, Christopher M. Schafer, John T. Powell, Karla K. Rodgers, Blaine H. M. Mooers, Christopher M. West
Article
Biochemistry & Molecular Biology
Janeen L. Arbuckle, Negar S. Rahman, Shuying Zhao, William Rodgers, Karla K. Rodgers
Article
Biochemistry & Molecular Biology
Dibyendu Chakraborty, Karla K. Rodgers, Shannon M. Conley, Muna I. Naash
Article
Biochemistry & Molecular Biology
Srinivas Chollangi, Timothy Mather, Karla K. Rodgers, John D. Ash
JOURNAL OF BIOLOGICAL CHEMISTRY
(2012)
Article
Cell Biology
Vivek K. Gupta, Ammaji Rajala, Karla K. Rodgers, Raju V. S. Rajala
Article
Multidisciplinary Sciences
William Rodgers, Jennifer N. Byrum, Destiny A. Simpson, Walker Hoolehan, Karla K. Rodgers
Article
Immunology
Jennifer N. Byrum, Walker E. Hoolehan, Destiny A. Simpson, William Rodgers, Karla K. Rodgers
Summary: The study showed that RAG2 plays a role in cellular responses to DNA double strand breaks by undergoing export from the nucleus and enrichment at the centrosome. Overexpression of full length RAG2 increased apoptosis levels in pre-B cells following irradiation, but also improved the rate of recovery after DNA damage.
Article
Biochemistry & Molecular Biology
Walker Hoolehan, Justin C. Harris, Jennifer N. Byrum, Destiny A. Simpson, Karla K. Rodgers
Summary: V(D)J recombination plays a crucial role in generating a diverse antigen receptor repertoire. Studies have found that the specificity of RAG1/2 for RSS heptamers is primarily determined by DNA structural features dependent on the purine/pyrimidine pattern.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Asif Alam Chowdhury, Karla Rodgers, Nachiket M. Godbole, Shanjana Awasthi
Summary: In this study, the stability and structure-activity relationship of the SPA4 peptide were investigated under different conditions. The results showed that the SPA4 peptide remained structurally stable at room temperature and 4°C, with minimal changes in pH, temperature, simulated lung fluids, and chemical components. Additionally, it was found that the SPA4 peptide retained its anti-inflammatory activity in the presence of lactate, which has important implications for its clinical application.