Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination [Cell Biology]
Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease, produces the majority of crossovers during meiotic HR, but it remains elusive whether mismatch repair factors promote HR in nonmeiotic cells. We disrupted genes encoding the MLH3 and PMS2 endonucleases in the human B cell line, TK6, generating null MLH3−/− and PMS2−/− muta...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Md Maminur Rahman, Mohiuddin Mohiuddin, Islam Shamima Keka, Kousei Yamada, Masataka Tsuda, Hiroyuki Sasanuma, Jessica Andreani, Raphael Guerois, Valerie Borde, Jean-Baptiste Charbonnier, Shunichi Takeda Tags: DNA and Chromosomes Source Type: research
Methylarginine metabolites are associated with attenuated muscle protein synthesis in cancer-associated muscle wasting [Protein Synthesis and Degradation]
Cancer cachexia is characterized by reductions in peripheral lean muscle mass. Prior studies have primarily focused on increased protein breakdown as the driver of cancer-associated muscle wasting. Therapeutic interventions targeting catabolic pathways have, however, largely failed to preserve muscle mass in cachexia, suggesting that other mechanisms might be involved. In pursuit of novel pathways, we used untargeted metabolomics to search for metabolite signatures that may be linked with muscle atrophy. We injected 7-week–old C57/BL6 mice with LLC1 tumor cells or vehicle. After 21 days, tumor-bearing mice exhibited redu...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Hawley E. Kunz, Jessica M. Dorschner, Taylor E. Berent, Thomas Meyer, Xuewei Wang, Aminah Jatoi, Rajiv Kumar, Ian R. Lanza Tags: Metabolism Source Type: research
Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation [Molecular Biophysics]
Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Suparno Nandi, Mortezaali Razzaghi, Dhiraj Srivastava, Mishtu Dey Tags: Enzymology Source Type: research
N-acetylglucosamine drives myelination by triggering oligodendrocyte precursor cell differentiation [Molecular Bases of Disease]
Myelination plays an important role in cognitive development and in demyelinating diseases like multiple sclerosis (MS), where failure of remyelination promotes permanent neuro-axonal damage. Modification of cell surface receptors with branched N-glycans coordinates cell growth and differentiation by controlling glycoprotein clustering, signaling, and endocytosis. GlcNAc is a rate-limiting metabolite for N-glycan branching. Here we report that GlcNAc and N-glycan branching trigger oligodendrogenesis from precursor cells by inhibiting platelet-derived growth factor receptor-α cell endocytosis. Supplying oral GlcNAc to lact...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Michael Sy, Alexander U. Brandt, Sung-Uk Lee, Barbara L. Newton, Judy Pawling, Autreen Golzar, Anas M. A. Rahman, Zhaoxia Yu, Graham Cooper, Michael Scheel, Friedemann Paul, James W. Dennis, Michael Demetriou Tags: Glycobiology and Extracellular Matrices Source Type: research
Mapping invisible epitopes by NMR spectroscopy [Molecular Biophysics]
Defining discontinuous antigenic epitopes remains a substantial challenge, as exemplified by the case of lipid transfer polyproteins, which are common pollen allergens. Hydrogen/deuterium exchange monitored by NMR can be used to map epitopes onto folded protein surfaces, but only if the complex rapidly dissociates. Modifying the standard NMR-exchange measurement to detect substoichiometric complexes overcomes this time scale limitation and provides new insights into recognition of lipid transfer polyprotein by antibodies. In the future, this new and exciting development should see broad application to a range of tight macr...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Emery T. Usher, Scott A. Showalter Tags: Editors ' Picks Highlights Source Type: research
Hydrogen/deuterium exchange memory NMR reveals structural epitopes involved in IgE cross-reactivity of allergenic lipid transfer proteins [Protein Structure and Folding]
Identification of antibody-binding epitopes is crucial to understand immunological mechanisms. It is of particular interest for allergenic proteins with high cross-reactivity as observed in the lipid transfer protein (LTP) syndrome, which is characterized by severe allergic reactions. Art v 3, a pollen LTP from mugwort, is frequently involved in this cross-reactivity, but no antibody-binding epitopes have been determined so far. To reveal human IgE-binding regions of Art v 3, we produced three murine high-affinity mAbs, which showed 70–90% coverage of the allergenic epitopes from mugwort pollen–allergic patients. As re...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Martina Di Muzio, Sabrina Wildner, Sara Huber, Michael Hauser, Eva Vejvar, Werner Auzinger, Christof Regl, Josef Laimer, Danila Zennaro, Nicole Wopfer, Christian G. Huber, Ronald van Ree, Adriano Mari, Peter Lackner, Fatima Ferreira, Mario Schubert, Gabri Tags: Editors ' Picks Source Type: research
FRET and optical trapping reveal mechanisms of actin activation of the power stroke and phosphate release in myosin V [Enzymology]
Myosins generate force and motion by precisely coordinating their mechanical and chemical cycles, but the nature and timing of this coordination remains controversial. We utilized a FRET approach to examine the kinetics of structural changes in the force-generating lever arm in myosin V. We directly compared the FRET results with single-molecule mechanical events examined by optical trapping. We introduced a mutation (S217A) in the conserved switch I region of the active site to examine how myosin couples structural changes in the actin- and nucleotide-binding regions with force generation. Specifically, S217A enhanced the...
Source: Journal of Biological Chemistry - December 18, 2020 Category: Chemistry Authors: Laura K. Gunther, John A. Rohde, Wanjian Tang, Joseph A. Cirilo Jr., Christopher P. Marang, Brent D. Scott, David D. Thomas, Edward P. Debold, Christopher M. Yengo Tags: Editors ' Picks Source Type: research
Correction: Functional domain and motif analyses of androgen receptor coregulator ARA70 and its differential expression in prostate cancer. [Additions and Corrections]
VOLUME 279 (2004) PAGES 33438–33446For Fig. 1B, the second, third, and fifth panels were mistakenly duplicated during article preparation as no yeast colonies were observed in these conditions. The corrected images are presented in the revised Fig. 1B. This correction does not affect the results or conclusions of the work. The authors apologize for the error.jbc;295/50/17382/F1F1F1Figure 1B. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Yueh-Chiang Hu, Shuyuan Yeh, Shauh-Der Yeh, Erik R. Sampson, Jiaoti Huang, Peng Li, Cheng-Lung Hsu, Huei-Ju Ting, Hui-Kuan Lin, Liang Wang, Eungseok Kim, Jing Ni, Chawnshang Chang Tags: Additions and Corrections Source Type: research
Withdrawal: FGF16 promotes invasive behavior of SKOV-3 ovarian cancer cells through activation of mitogen-activated protein kinase (MAPK) signaling pathway. [Withdrawals/Retractions]
This article has been withdrawn by the authors. There were undeclared splices in Fig. 2 (d and e). In addition, the bands in Fig. 2e are shown as migrating at the same molecular weight; however, upon analysis of the original data, they were migrating at different molecular weights. The immunoblots of Fig. 4b active β-catenin and Fig. 8B CaMKII of Basu and Roy (2013) J. Biol. Chem. 288, 4355–4367 have been reused as Fig. 5g, corresponding to FGF16, and as Fig. 6a, corresponding to tubulin, respectively. Panels A and D from Fig. 6e presented the same data with different brightness. The authors affirm that the experiments ...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Moitri Basu, Satinath Mukhopadhyay, Uttara Chatterjee, Sib Sankar Roy Tags: Withdrawals/Retractions Source Type: research
Mycobacteria excise DNA damage in 12- or 13-nucleotide-long oligomers by prokaryotic-type dual incisions and performs transcription-coupled repair [Genomics and Proteomics]
In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual-incision patterns have been discovered: the prokaryotic type, which removes the damage in 11–13-nucleotide-long oligomers, and the eukaryotic type, which removes the damage in 24–32-nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising from in...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Christopher P. Selby, Laura A. Lindsey-Boltz, Yanyan Yang, Aziz Sancar Tags: Accelerated Communications Source Type: research
Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography [Enzymology]
The main protease (3CL Mpro) from SARS–CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication. 3CL Mpro possesses an unusual catalytic dyad composed of Cys145 and His41 residues. A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active-site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus. Here, we present the room-temperature neutron structure of 3CL Mpro, which allowed direct determination of hydrogen atom posi...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Daniel W. Kneller, Gwyndalyn Phillips, Kevin L. Weiss, Swati Pant, Qiu Zhang, Hugh M. O'Neill, Leighton Coates, Andrey Kovalevsky Tags: Molecular Bases of Disease Source Type: research
Post-translational regulation of the maȷor drug transporters in the families of organic anion transporters and organic anion-transporting polypeptides [Protein Structure and Folding]
The organic anion transporters (OATs) and organic anion–transporting polypeptides (OATPs) belong to the solute carrier (SLC) transporter superfamily and play important roles in handling various endogenous and exogenous compounds of anionic charge. The OATs and OATPs are often implicated in drug therapy by impacting the pharmacokinetics of clinically important drugs and, thereby, drug exposure in the target organs or cells. Various mechanisms (e.g. genetic, environmental, and disease-related factors, drug-drug interactions, and food-drug interactions) can lead to variations in the expression and activity of the anion drug...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Wooin Lee, Jeong-min Ha, Yuichi Sugiyama Tags: JBC Reviews Source Type: research
Site-specific contacts enable distinct modes of TRPV1 regulation by the potassium channel Kv{beta}1 subunit [Molecular Biophysics]
Transient receptor potential vanilloid 1 (TRPV1) channel is a multimodal receptor that is responsible for nociceptive, thermal, and mechanical sensations. However, which biomolecular partners specifically interact with TRPV1 remains to be elucidated. Here, we used cDNA library screening of genes from mouse dorsal root ganglia combined with patch-clamp electrophysiology to identify the voltage-gated potassium channel auxiliary subunit Kvβ1 physically interacting with TRPV1 channel and regulating its function. The interaction was validated in situ using endogenous dorsal root ganglia neurons, as well as a recombinant expres...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Yuanyuan Wang, Xiaoyi Mo, Conghui Ping, Qian Huang, Hao Zhang, Chang Xie, Bo Zhong, Dongdong Li, Jing Yao Tags: Cell Biology Source Type: research
A trade-off switch of two immunological memories in Caenorhabditis elegans reinfected by bacterial pathogens [Microbiology]
Recent studies have suggested that innate immune responses exhibit characteristics associated with memory linked to modulations in both vertebrates and invertebrates. However, the diverse evolutionary paths taken, particularly within the invertebrate taxa, should lead to similarly diverse innate immunity memory processes. Our understanding of innate immune memory in invertebrates primarily comes from studies of the fruit fly Drosophila melanogaster, the generality of which is unclear. Caenorhabditis elegans typically inhabits soil harboring a variety of fatal microbial pathogens; for this invertebrate, the innate immune sy...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Jinyuan Yan, Ninghui Zhao, Zhongshan Yang, Yuhong Li, Hua Bai, Wei Zou, Keqin Zhang, Xiaowei Huang Tags: Immunology Source Type: research
CDKN2A/p16INK4a suppresses hepatic fatty acid oxidation through the AMPK{alpha}2-SIRT1-PPAR{alpha} signaling pathway [Metabolism]
In addition to their well-known role in the control of cellular proliferation and cancer, cell cycle regulators are increasingly identified as important metabolic modulators. Several GWAS have identified SNPs near CDKN2A, the locus encoding for p16INK4a (p16), associated with elevated risk for cardiovascular diseases and type-2 diabetes development, two pathologies associated with impaired hepatic lipid metabolism. Although p16 was recently shown to control hepatic glucose homeostasis, it is unknown whether p16 also controls hepatic lipid metabolism. Using a combination of in vivo and in vitro approaches, we found that p16...
Source: Journal of Biological Chemistry - December 11, 2020 Category: Chemistry Authors: Yann Deleye, Alexia Karen Cotte, Sarah Anissa Hannou, Nathalie Hennuyer, Lucie Bernard, Bruno Derudas, Sandrine Caron, Vanessa Legry, Emmanuelle Vallez, Emilie Dorchies, Nathalie Martin, Steve Lancel, Jean Sebastien Annicotte, Kadiombo Bantubungi, Albin P Tags: Metabolism Source Type: research
