2021 JBC Herbert Tabor Early Career Investigator Awards: Call for nominations [Editorials]
One of our favorite times of the year has arrived: starting the process of selecting this year's JBC Herbert Tabor Early Career Investigator (JHTECI) Awardees. It's a favorite time because we love combing through all of the great science published in JBC in the past year, identifying the rising stars in biological chemistry worldwide, and reminding ourselves of the exciting new insights and advances that we've gotten to play a part in sharing with the scientific community. It is inspiring to learn about the creative strategies and amazing techniques that our authors employed to tackle their topics. And it's fun to dig thro...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Lila M. Gierasch, George N. DeMartino Tags: Editorials Source Type: research

Withdrawal: Active participation of cellular chaperone Hsp90 in regulating the function of rotavirus nonstructural protein 3 (NSP3). [Withdrawals/Retractions]
This article has been withdrawn by the authors. The Journal determined that there are similar repetitive features in the background area of Figs. 4B, 5B, 6B, and 7A and Fig. S4, but the authors do not agree to the raised concerns. The authors state that they provided uncropped scans of the autoradiograms from the corresponding and/or replicate experiments done at same time of the original experiments. The authors state that due to the tropical climate, the quality of the autoradiograms may have partially deteriorated as the work was done more than 10 years ago, but still they could not visualize any repetitive elements in ...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Dipanjan Dutta, Shiladitya Chattopadhyay, Parikshit Bagchi, Umesh Chandra Halder, Satabdi Nandi, Anupam Mukherjee, Nobumichi Kobayashi, Koki Taniguchi, Mamta Chawla-Sarkar Tags: Withdrawals/Retractions Source Type: research

Withdrawal: Effect of Ser-129 phosphorylation on interaction of {alpha}-synuclein with synaptic and cellular membranes. [Withdrawals/Retractions]
This article has been withdrawn by Naomi Visanji, Sabine Wislet-Gendebien, Loren Oschipok, Isabelle Aubert, Paul Fraser, and Anurag Tandon. Gang Zhang was not reachable. The pS129 immunoblot in Fig. 1 was used for both membrane and cytosol fractions. In Fig. 4B, the pS129 blots from representative WT and A30P tissues are the same. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Naomi P. Visanji, Sabine Wislet-Gendebien, Loren W. Oschipok, Gang Zhang, Isabelle Aubert, Paul E. Fraser, Anurag Tandon Tags: Withdrawals/Retractions Source Type: research

Withdrawal: Cytosolic proteins regulate {alpha}-synuclein dissociation from presynaptic membranes. [Withdrawals/Retractions]
This article has been withdrawn by Sabine Wislet-Gendebien, Cheryl D'Souza, Toshitaka Kawarai, Peter St George-Hyslop, David Westaway, Paul Fraser, and Anurag Tandon. The α-synuclein and GAPDH bands at 30 min were superimposed on the earlier time points in Fig. 1B. The GAPDH bands in Fig. 4B were reused in Fig. 7A. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Sabine Wislet-Gendebien, Cheryl D'Souza, Toshitaka Kawarai, Peter St George-Hyslop, David Westaway, Paul Fraser, Anurag Tandon Tags: Withdrawals/Retractions Source Type: research

Withdrawal: hPEBP4 resists TRAIL-induced apoptosis of human prostate cancer cells by activating Akt and deactivating ERK1/2 pathways. [Withdrawals/Retractions]
This article has been withdrawn by the authors except for Hongzhe Li, who could not be reached. In Fig. 2C, lanes 7 and 14 of the p-ERK1/2 immunoblot are the same. In Fig. 2F, the upper p-ERK1/2 bands in lanes 3 and 4 are the same. Portions of the actin immunoblot from Fig. 2C are reused in Fig. 2, E and F. There are several duplicated features in the FACS plots shown in Fig. 3 (A and B). Portions of the Procaspase 3 immunoblot in Fig. 4B were reused in Procaspase 3 and BID immunoblots in Fig. 4D. The withdrawing authors do not agree with the Journal's analysis of Fig. 2G and Fig. 4 (C and E). The withdrawing authors state...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Hongzhe Li, Xiaojian Wang, Nan Li, Jianming Qiu, Yuanyuan Zhang, Xuetao Cao Tags: Withdrawals/Retractions Source Type: research

Withdrawal: A novel human phosphatidylethanolamine-binding protein resists tumor necrosis factor {alpha}-induced apoptosis by inhibiting mitogen-activated protein kinase pathway activation and phosphatidylethanolamine externalization. [Withdrawals/Retractions]
This article has been withdrawn by the authors except for Hongzhe Li, who could not be reached. In Fig. 2A, lanes 3 and 4 of the hPEBP4 panel and lanes 3, 4, and 6 of the actin panel are the same. In the hPEBP4 panel of Fig. 2B, the last two lanes are the same. In the actin panel for the same figure, lanes 3 and 4 are duplicates and lanes 6 and 7 are duplicates. In Fig. 2C, lanes 3 and 4 of the actin panel are duplicates. Lanes 8 and 9 of the same panel are duplicates. Lanes 1 and 3 of the myc immunoblot in Fig. 3C are the same. The last lane of the actin immunoblot in Fig. 4A was reused in the first lane of the actin immu...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Xiaojian Wang, Nan Li, Bin Liu, Hongying Sun, Taoyong Chen, Hongzhe Li, Jianming Qiu, Lihuang Zhang, Tao Wan, Xuetao Cao Tags: Withdrawals/Retractions Source Type: research

Withdrawal: Nuclear factor-{kappa}B p65 facilitates longitudinal bone growth by inducing growth plate chondrocyte proliferation and differentiation and by preventing apoptosis. [Withdrawals/Retractions]
This article has been withdrawn by Shufang Wu, Geoffrey Rezvani, and Francesco De Luca. Doris Fadoju could not be reached. Fig. 3F was reused from Wu, S., et al. (2006) J. Biol. Chem. 281, 51250–5127. Lanes 2 and 3 of Fig. 4A are the same. The actin immunoblots in Figs. 5D and 8F are the same. The β-actin panel from Fig. 5C was reused in Fig. 7A. Portions of the actin immunoblot in Fig. 5E were reused in Fig. 5F and Fig. S7. The first lane of the BMP-2 immunoblot in Fig. 7E was reused in Fig. 7F. Additionally, a portion of the actin immunoblot in Fig. 7E was reused in Fig. 7F. Portions of Fig. S5 were reused in ...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Shufang Wu, Janna K. Flint, Geoffrey Rezvani, Francesco De Luca Tags: Withdrawals/Retractions Source Type: research

The transcription factor PITX1 drives astrocyte differentiation by regulating the SOX9 gene [Gene Regulation]
Astrocytes perform multiple essential functions in the developing and mature brain, including regulation of synapse formation, control of neurotransmitter release and uptake, and maintenance of extracellular ion balance. As a result, astrocytes have been implicated in the progression of neurodegenerative disorders such as Alzheimer's disease, Huntington's disease, and Parkinson's disease. Despite these critical functions, the study of human astrocytes can be difficult because standard differentiation protocols are time-consuming and technically challenging, but a differentiation protocol recently developed in our laborator...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Jeong Su Byun, Mihee Oh, Seonha Lee, Jung-Eun Gil, Yeajin Mo, Bonsu Ku, Won-Kon Kim, Kyoung-Jin Oh, Eun-Woo Lee, Kwang-Hee Bae, Sang Chul Lee, Baek-Soo Han Tags: Developmental Biology Source Type: research

FmhA and FmhC of Staphylococcus aureus incorporate serine residues into peptidoglycan cross-bridges [Microbiology]
Staphylococcal peptidoglycan is characterized by pentaglycine cross-bridges that are cross-linked between adjacent wall peptides by penicillin-binding proteins to confer robustness and flexibility. In Staphylococcus aureus, pentaglycine cross-bridges are synthesized by three proteins: FemX adds the first glycine, and the homodimers FemA and FemB sequentially add two Gly-Gly dipeptides. Occasionally, serine residues are also incorporated into the cross-bridges by enzymes that have heretofore not been identified. Here, we show that the FemA/FemB homologues FmhA and FmhC pair with FemA and FemB to incorporate Gly-Ser dipeptid...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Stephanie Willing, Emma Dyer, Olaf Schneewind, Dominique Missiakas Tags: Microbiology Source Type: research

Development of Noonan syndrome by deregulation of allosteric SOS autoactivation [Cell Biology]
Ras family proteins play an essential role in several cellular functions, including growth, differentiation, and survival. The mechanism of action of Ras mutants in Costello syndrome and cancers has been identified, but the contribution of Ras mutants to Noonan syndrome, a genetic disorder that prevents normal development in various parts of the body, is unknown. Son of Sevenless (SOS) is a Ras guanine nucleotide exchange factor. In response to Ras-activating cell signaling, SOS autoinhibition is released and is followed by accelerative allosteric feedback autoactivation. Here, using mutagenesis-based kinetic and pulldown ...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Hope Gloria Umutesi, Hanh My Hoang, Hope Elizabeth Johnson, Kwangho Nam, Jongyun Heo Tags: Enzymology Source Type: research

Progranulin modulates cartilage-specific gene expression via sirtuin 1-mediated deacetylation of the transcription factors SOX9 and P65 [Gene Regulation]
In conclusion, our findings reveal a mechanism of action for PGRN that maintains cartilage homeostasis and supports the notion that PGRN up-regulation may be a promising strategy for managing OA. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Dongxu Feng, Xiaomin Kang, Ruiqi Wang, He Chen, Kun Zhang, Weilou Feng, Huixia Li, Yangjun Zhu, Shufang Wu Tags: Cell Biology Source Type: research

Substrate recognition induces sequential electron transfer across subunits in the nitrogenase-like DPOR complex [Molecular Biophysics]
A key step in bacteriochlorophyll biosynthesis is the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), catalyzed by dark-operative protochlorophyllide oxidoreductase (DPOR). DPOR is made of electron donor (BchL) and acceptor (BchNB) component proteins. BchNB is further composed of two subunits each of BchN and BchB arranged as an α2β2 heterotetramer with two active sites for substrate reduction. Such oligomeric architectures are found in several other electron transfer (ET) complexes, but how this architecture influences activity is unclear. Here, we describe allosteric communication betwee...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Elliot I. Corless, Brian Bennett, Edwin Antony Tags: Enzymology Source Type: research

Mediator complex subunit Med19 binds directly GATA transcription factors and is required with Med1 for GATA-driven gene regulation in vivo [Developmental Biology]
The evolutionarily conserved multiprotein Mediator complex (MED) serves as an interface between DNA-bound transcription factors (TFs) and the RNA Pol II machinery. It has been proposed that each TF interacts with a dedicated MED subunit to induce specific transcriptional responses. But are these binary partnerships sufficient to mediate TF functions? We have previously established that the Med1 Mediator subunit serves as a cofactor of GATA TFs in Drosophila, as shown in mammals. Here, we observe mutant phenotype similarities between another subunit, Med19, and the Drosophila GATA TF Pannier (Pnr), suggesting functional int...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Clement Immarigeon, Sandra Bernat–Fabre, Emmanuelle Guillou, Alexis Verger, Elodie Prince, Mohamed A. Benmedȷahed, Adeline Payet, Marie Couralet, Didier Monte, Vincent Villeret, Henri–Marc Bourbon, Muriel Boube Tags: Gene Regulation Source Type: research

High-density lipoproteins are a potential therapeutic target for age-related macular degeneration [Lipids]
Strong evidence suggests that dysregulated lipid metabolism involving dysfunction of the retinal pigmented epithelium (RPE) underlies the pathogenesis of age-related macular degeneration (AMD), the leading cause of irreversible blindness in the elderly. A hallmark of AMD is the overproduction of lipid- and protein-rich extracellular deposits that accumulate in the extracellular matrix (Bruch's membrane (BrM)) adjacent to the RPE. We analyzed apolipoprotein A-1 (ApoA-1)-containing lipoproteins isolated from BrM of elderly human donor eyes and found a unique proteome, distinct from high-density lipoprotein (HDL) isolated fro...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Una L. Kelly, Daniel Grigsby, Martha A. Cady, Michael Landowski, Nikolai P. Skiba, Jian Liu, Alan T. Remaley, Mikael Klingeborn, Catherine Bowes Rickman Tags: Cell Biology Source Type: research

The insufficiency of ATG4A in macroautophagy [Membrane Biology]
During autophagy, LC3 and GABARAP proteins become covalently attached to phosphatidylethanolamine on the growing autophagosome. This attachment is also reversible. Deconjugation (or delipidation) involves the proteolytic cleavage of an isopeptide bond between LC3 or GABARAP and the phosphatidylethanolamine headgroup. This cleavage is carried about by the ATG4 family of proteases (ATG4A, B, C, and D). Many studies have established that ATG4B is the most active of these proteases and is sufficient for autophagy progression in simple cells. Here we examined the second most active protease, ATG4A, to map out key regulatory mot...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Nathan Nguyen, Taryn J. Olivas, Antonio Mires, Jiaxin Jin, Shenliang Yu, Lin Luan, Shanta Nag, Karlina J. Kauffman, Thomas J. Melia Tags: Cell Biology Source Type: research

Structural analysis of the LDL receptor-interacting FERM domain in the E3 ubiquitin ligase IDOL reveals an obscured substrate-binding site [Metabolism]
Hepatic abundance of the low-density lipoprotein receptor (LDLR) is a critical determinant of circulating plasma LDL cholesterol levels and hence development of coronary artery disease. The sterol-responsive E3 ubiquitin ligase inducible degrader of the LDLR (IDOL) specifically promotes ubiquitination and subsequent lysosomal degradation of the LDLR and thus controls cellular LDL uptake. IDOL contains an extended N-terminal FERM (4.1 protein, ezrin, radixin, and moesin) domain, responsible for substrate recognition and plasma membrane association, and a second C-terminal RING domain, responsible for the E3 ligase activity ...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Luca Martinelli, Athanassios Adamopoulos, Patrik Johansson, Paul T. Wan, Jenny Gunnarsson, Hongwei Guo, Helen Boyd, Noam Zelcer, Titia K. Sixma Tags: Protein Structure and Folding Source Type: research

Intermittent enzyme replacement therapy prevents Neu1 deficiency [Cell Biology]
Mutations in the galactosidase β 1 (GLB1) gene cause lysosomal β-galactosidase (β-Gal) deficiency and clinical onset of the neurodegenerative lysosomal storage disease, GM1 gangliosidosis. β-Gal and neuraminidase 1 (NEU1) form a multienzyme complex in lysosomes along with the molecular chaperone, protective protein cathepsin A (PPCA). NEU1 is deficient in the neurodegenerative lysosomal storage disease sialidosis, and its targeting to and stability in lysosomes strictly depend on PPCA. In contrast, β-Gal only partially depends on PPCA, prompting us to investigate the role that β-Gal plays in t...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Amanda R. Luu, Cara Wong, Vishal Agrawal, Nathan Wise, Britta Handyside, Melanie J. Lo, Glenn Pacheco, Jessica B. Felix, Alexander Giaramita, Alessandra d'Azzo, Jon Vincelette, Sherry Bullens, Stuart Bunting, Terri M. Christianson, Charles M. Hague, Jonat Tags: Molecular Bases of Disease Source Type: research

Intracerebroventricular enzyme replacement therapy with {beta}-galactosidase reverses brain pathologies due to GM1 gangliosidosis in mice [Enzymology]
Autosomal recessive mutations in the galactosidase β1 (GLB1) gene cause lysosomal β-gal deficiency, resulting in accumulation of galactose-containing substrates and onset of the progressive and fatal neurodegenerative lysosomal storage disease, GM1 gangliosidosis. Here, an enzyme replacement therapy (ERT) approach in fibroblasts from GM1 gangliosidosis patients with recombinant human β-gal (rhβ-gal) produced in Chinese hamster ovary cells enabled direct and precise rhβ-gal delivery to acidified lysosomes. A single, low dose (3 nm) of rhβ-gal was sufficient for normalizing β-gal activity a...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Joseph C. Chen, Amanda R. Luu, Nathan Wise, Rolando De Angelis, Vishal Agrawal, Linley Mangini, Jon Vincelette, Britta Handyside, Harry Sterling, Melanie J. Lo, Hio Wong, Nicole Galicia, Glenn Pacheco, Jeremy Van Vleet, Alexander Giaramita, Sylvia Fong, S Tags: Cell Biology Source Type: research

Multimodal small-molecule screening for human prion protein binders [Molecular Bases of Disease]
Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19F-observed and saturation transfer difference (STD) NMR spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection,...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Andrew G. Reidenbach, Michael F. Mesleh, Dominick Casalena, Sonia M. Vallabh, Jayme L. Dahlin, Alison J. Leed, Alix I. Chan, Dmitry L. Usanov, Jenna B. Yehl, Christopher T. Lemke, Arthur J. Campbell, Rishi N. Shah, Om K. Shrestha, Joshua R. Sacher, Victor Tags: Molecular Biophysics Source Type: research

Adaptation induced by self-targeting in a type I-B CRISPR-Cas system [RNA]
Haloferax volcanii is, to our knowledge, the only prokaryote known to tolerate CRISPR-Cas–mediated damage to its genome in the WT background; the resulting cleavage of the genome is repaired by homologous recombination restoring the WT version. In mutant Haloferax strains with enhanced self-targeting, cell fitness decreases and microhomology-mediated end joining becomes active, generating deletions in the targeted gene. Here we use self-targeting to investigate adaptation in H. volcanii CRISPR-Cas type I-B. We show that self-targeting and genome breakage events that are induced by self-targeting, such as those cataly...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Aris–Edda Stachler, Julia Wortz, Omer S. Alkhnbashi, Israela Turgeman–Grott, Rachel Smith, Thorsten Allers, Rolf Backofen, Uri Gophna, Anita Marchfelder Tags: Microbiology Source Type: research

X-ray-induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner [Protein Structure and Folding]
Since the advent of protein crystallography, atomic-level macromolecular structures have provided a basis to understand biological function. Enzymologists use detailed structural insights on ligand coordination, interatomic distances, and positioning of catalytic amino acids to rationalize the underlying electronic reaction mechanisms. Often the proteins in question catalyze redox reactions using metal cofactors that are explicitly intertwined with their function. In these cases, the exact nature of the coordination sphere and the oxidation state of the metal is of utmost importance. Unfortunately, the redox-active nature ...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Vera Pfanzagl, John H. Beale, Hanna Michlits, Daniel Schmidt, Thomas Gabler, Christian Obinger, Kristina Dȷinović–Carugo, Stefan Hofbauer Tags: Enzymology Source Type: research

The mechano-sensitive response of {beta}1 integrin promotes SRC-positive late endosome recycling and activation of Yes-associated protein [Signal Transduction]
Yes-associated protein (YAP) signaling has emerged as a crucial pathway in several normal and pathological processes. Although the main upstream effectors that regulate its activity have been extensively studied, the role of the endosomal system has been far less characterized. Here, we identified the late endosomal/lysosomal adaptor MAPK and mTOR activator (LAMTOR) complex as an important regulator of YAP signaling in a preosteoblast cell line. We found that p18/LAMTOR1-mediated peripheral positioning of late endosomes allows delivery of SRC proto-oncogene, nonreceptor tyrosine kinase (SRC) to the plasma membrane and prom...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Marc R. Block, Molly Brunner, Theo Ziegelmeyer, Dominique Lallemand, Mylene Pezet, Genevieve Chevalier, Philippe Ronde, Cecile Gauthier–Rouviere, Bernhard Wehrle–Haller, Daniel Bouvard Tags: Cell Biology Source Type: research

Findings in redox biology: From H2O2 to oxidative stress [Metabolism]
My interest in biological chemistry proceeded from enzymology in vitro to the study of physiological chemistry in vivo. Investigating biological redox reactions, I identified hydrogen peroxide (H2O2) as a normal constituent of aerobic life in eukaryotic cells. This finding led to developments that recognized the essential role of H2O2 in metabolic redox control. Further research included studies on GSH, toxicological aspects (the concept of “redox cycling”), biochemical pharmacology (ebselen), nutritional biochemistry and micronutrients (selenium, carotenoids, flavonoids), and the concept of “oxidative st...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Helmut Sies Tags: Reflections Source Type: research

Iron homeostasis and plant immune responses: Recent insights and translational implications [Immunology]
Iron metabolism and the plant immune system are both critical for plant vigor in natural ecosystems and for reliable agricultural productivity. Mechanistic studies of plant iron home-ostasis and plant immunity have traditionally been carried out in isolation from each other; however, our growing understanding of both processes has uncovered significant connections. For example, iron plays a critical role in the generation of reactive oxygen intermediates during immunity and has been recently implicated as a critical factor for immune-initiated cell death via ferroptosis. Moreover, plant iron stress triggers immune activati...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: John H. Herlihy, Terri A. Long, John M. McDowell Tags: JBC Reviews Source Type: research

Mechanistic cross-talk between DNA/RNA polymerase enzyme kinetics and nucleotide substrate availability in cells: Implications for polymerase inhibitor discovery [Metabolism]
Enzyme kinetic analysis reveals a dynamic relationship between enzymes and their substrates. Overall enzyme activity can be controlled by both protein expression and various cellular regulatory systems. Interestingly, the availability and concentrations of intracellular substrates can constantly change, depending on conditions and cell types. Here, we review previously reported enzyme kinetic parameters of cellular and viral DNA and RNA polymerases with respect to cellular levels of their nucleotide substrates. This broad perspective exposes a remarkable co-evolution scenario of DNA polymerase enzyme kinetics with dNTP lev...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Si'Ana A. Coggins, Bijan Mahboubi, Raymond F. Schinazi, Baek Kim Tags: JBC Reviews Source Type: research

Phase separation drives decision making in cell division [DNA and Chromosomes]
Liquid–liquid phase separation (LLPS) of biomolecules drives the formation of subcellular compartments with distinct physicochemical properties. These compartments, free of lipid bilayers and therefore called membraneless organelles, include nucleoli, centrosomes, heterochromatin, and centromeres. These have emerged as a new paradigm to account for subcellular organization and cell fate decisions. Here we summarize recent studies linking LLPS to mitotic spindle, heterochromatin, and centromere assembly and their plasticity controls in the context of the cell division cycle, highlighting a functional role for phase be...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Xing Liu, Haowei Wang, Zhen Dou, Ke Ruan, Donald L. Hill, Lin Li, Yunyu Shi, Xuebiao Yao Tags: JBC Reviews Source Type: research

Heterogeneous adaptation of cysteine reactivity to a covalent oncometabolite [Metabolism]
An important context in which metabolism influences tumorigenesis is the genetic cancer syndrome hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a disease in which mutation of the tricarboxylic acid cycle enzyme fumarate hydratase (FH) causes hyperaccumulation of fumarate. This electrophilic oncometabolite can alter gene activity at the level of transcription, via reversible inhibition of epigenetic dioxygenases, as well as posttranslationally, via covalent modification of cysteine residues. To better understand the potential for metabolites to influence posttranslational modifications important to tumorigenesi...
Source: Journal of Biological Chemistry - September 25, 2020 Category: Chemistry Authors: Minervo Perez, Daniel W. Bak, Sarah E. Bergholtz, Daniel R. Crooks, Bhargav Srinivas Arimilli, Youfeng Yang, Eranthie Weerapana, W. Marston Linehan, Jordan L. Meier Tags: Accelerated Communications Source Type: research

In JBC we trust [Editorials]
Peer Review Week (September 21–25 this year) serves as an annual reminder to thank referees for their service to the scientific community. We hope we express our appreciation and acknowledge in an ongoing way the central role of peer review in science publishing, but we will take this annual reminder to say “THANK YOU” to JBC's Editorial Board Members (EBMs) and to the other reviewers who help us maintain the quality and reliability of JBC's content.The theme of this year's Peer Review Week—Trust in Peer Review (1)—hits especially close to home for those of us involved in JBC. When I began my ...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Lila M. Gierasch Tags: Editorials Source Type: research

Correction: The RNA-binding protein HuD regulates autophagosome formation in pancreatic {beta} cells by promoting autophagy-related gene 5 expression. [Additions and Corrections]
VOLUME 289 (2013) PAGES 112–121The autophagy flux experiments shown in Figs. 2D and 4A were performed similarly, either by serial transfection of pcDNA or pHuD followed by transfection with the GFP reporter construct or by single transfection of pcDNA or pHuD. No difference was observed with either method. As no difference was observed, the HuD and actin immunoblots from Fig. 2D were mistakenly used in Fig. 4A. The corrected Fig. 4A now shows results from a single transfection rather than a serial transfection. The quantification has also been corrected. This correction does not affect the results or conclusions of t...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Chongtae Kim, Wook Kim, Heejin Lee, Eunbyul Ji, Yun-Jeong Choe, Jennifer L. Martindale, Wado Akamatsu, Hideyuki Okano, Ho-Shik Kim, Suk Woo Nam, Myriam Gorospe, Eun Kyung Lee Tags: Additions and Corrections Source Type: research

Retraction: Inhibition of histone deacetylase activity promotes invasion of human cancer cells through activation of urokinase plasminogen activator. [Withdrawals/Retractions]
This article has been retracted by the publisher. None of the authors could be reached for comment. The last three lanes of the actin panel from SK-N-AS cells in Fig. 2B were reused in the first three lanes of the HDAC1 panel in Fig. 7A. In Fig. 6A, the HDAC5 and HDAC7 immunoblots are the same. A portion of the input panel from Fig. 6B was reused in the input panel for siHDAC1 in Fig. 7B. (Source: Journal of Biological Chemistry)
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Sai Murali Krishna Pulukuri, Bharathi Gorantla, Jasti S. Rao Tags: Withdrawals/Retractions Source Type: research

Lysocardiolipin acyltransferase regulates NSCLC cell proliferation and migration by modulating mitochondrial dynamics [Lipids]
In this study, in silico analysis of TCGA lung cancer data sets revealed a significant increase in LYCAT expression, which was later corroborated in human lung cancer tissues and immortalized lung cancer cell lines via indirect immunofluorescence and immunoblotting, respectively. Stable knockdown of LYCAT in NSCLC cell lines not only reduced CL and increased monolyso-CL levels but also reduced in vivo tumor growth, as determined by xenograft studies in athymic nude mice. Furthermore, blocking LYCAT activity using a LYCAT mimetic peptide attenuated cell migration, suggesting a novel role for LYCAT activity in promoting NSCL...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Long Shuang Huang, Sainath R. Kotha, Sreedevi Avasarala, Michelle VanScoyk, Robert A. Winn, Arjun Pennathur, Puttaraju S. Yashaswini, Mounica Bandela, Ravi Salgia, Yulia Y. Tyurina, Valerian E. Kagan, Xiangdong Zhu, Sekhar P. Reddy, Tara Sudhadevi, Prasan Tags: Molecular Bases of Disease Source Type: research

Modification of lipid rafts by extracellular vesicles carrying HIV-1 protein Nef induces redistribution of amyloid precursor protein and Tau, causing neuronal dysfunction [Microbiology]
In this study, we investigated how HIV-1 protein Nef secreted in extracellular vesicles (exNef) impairs neuronal functionality. ExNef were rapidly taken up by neural cells in vitro, reducing the abundance of ABC transporter A1 (ABCA1) and thus cholesterol efflux and increasing the abundance and modifying lipid rafts in neuronal plasma membranes. ExNef caused a redistribution of amyloid precursor protein (APP) and Tau to lipid rafts and increased the abundance of these proteins, as well as of Aβ42. ExNef further potentiated phosphorylation of Tau and activation of inflammatory pathways. These changes were accompanied b...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Michael Ditiatkovski, Nigora Mukhamedova, Dragana Dragoljevic, Anh Hoang, Hann Low, Tatiana Pushkarsky, Ying Fu, Irena Carmichael, Andrew F. Hill, Andrew J. Murphy, Michael Bukrinsky, Dmitri Sviridov Tags: Molecular Bases of Disease Source Type: research

Anterograde trafficking of ciliary MAP kinase-like ICK/CILK1 by the intraflagellar transport machinery is required for intraciliary retrograde protein trafficking [Cell Biology]
ICK (also known as CILK1) is a mitogen-activated protein kinase–like kinase localized at the ciliary tip. Its deficiency is known to result in the elongation of cilia and causes ciliopathies in humans. However, little is known about how ICK is transported to the ciliary tip. We here show that the C-terminal noncatalytic region of ICK interacts with the intraflagellar transport (IFT)–B complex of the IFT machinery and participates in its transport to the ciliary tip. Furthermore, total internal reflection fluorescence microscopy demonstrated that ICK undergoes bidirectional movement within cilia, similarly to IF...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Kentaro Nakamura, Tatsuro Noguchi, Mariko Takahara, Yoshihiro Omori, Takahisa Furukawa, Yohei Katoh, Kazuhisa Nakayama Tags: Cell Biology Source Type: research

EGFR forms ligand-independent oligomers that are distinct from the active state [Molecular Biophysics]
The human epidermal growth factor receptor (EGFR/ERBB1) is a receptor tyrosine kinase (RTK) that forms activated oligomers in response to ligand. Much evidence indicates that EGFR/ERBB1 also forms oligomers in the absence of ligand, but the structure and physiological role of these ligand-independent oligomers remain unclear. To examine these features, we use fluorescence microscopy to measure the oligomer stability and FRET efficiency for homo- and hetero-oligomers of fluorescent protein-labeled forms of EGFR and its paralog, human epidermal growth factor receptor 2 (HER2/ERBB2) in vesicles derived from mammalian cell mem...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Patrick O. Byrne, Kalina Hristova, Daniel J. Leahy Tags: Signal Transduction Source Type: research

15-Keto-PGE2 acts as a biased/partial agonist to terminate PGE2-evoked signaling [Computational Biology]
Prostaglandin E2 (PGE2) is well-known as an endogenous proinflammatory prostanoid synthesized from arachidonic acid by the activation of cyclooxygenase-2. E type prostanoid (EP) receptors are cognates for PGE2 that have four main subtypes: EP1 to EP4. Of these, the EP2 and EP4 prostanoid receptors have been shown to couple to Gαs-protein and can activate adenylyl cyclase to form cAMP. Studies suggest that EP4 receptors are involved in colorectal homeostasis and cancer development, but further work is needed to identify the roles of EP2 receptors in these functions. After sufficient inflammation has been evoked by PGE...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Suzu Endo, Akiko Suganami, Keijo Fukushima, Kanaho Senoo, Yumi Araki, John W. Regan, Masato Mashimo, Yutaka Tamura, Hiromichi Fujino Tags: Signal Transduction Source Type: research

Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue [RNA]
Translation termination in bacteria requires that the stop codon be recognized by release factor RF1 or RF2, leading to hydrolysis of the ester bond between the peptide and tRNA on the ribosome. As a consequence, normal termination cannot proceed if the translated mRNA lacks a stop codon. In Escherichia coli, the ribosome rescue factor ArfA releases the nascent polypeptide from the stalled ribosome with the help of RF2 in a stop codon–independent manner. Interestingly, the reaction does not proceed if RF1 is instead provided, even though the structures of RF1 and RF2 are very similar. Here, we identified the regions ...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Daisuke Kurita, Tatsuhiko Abo, Hyouta Himeno Tags: Protein Synthesis and Degradation Source Type: research

Long-term effects of the proline-rich antimicrobial peptide Oncocin112 on the Escherichia coli translation machinery [Cell Biology]
We present a superresolution fluorescence microscopy study of the long-term effects of Onc112 on ribosome, elongation factor-Tu (EF-Tu), and DNA spatial distributions and diffusive properties in intact Escherichia coli cells. The new data corroborate earlier mechanistic inferences from studies in vitro. Comparisons with the diffusive behavior induced by the ribosome-binding antibiotics chloramphenicol and kasugamycin show how the specific location of each agent's ribosomal binding site affects the long-term distribution of ribosomal species between 30S and 50S subunits versus 70S polysomes. Analysis of the single-step disp...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Yanyu Zhu, James C. Weisshaar, Mainak Mustafi Tags: Molecular Biophysics Source Type: research

Catastrophic actin filament bursting by cofilin, Aip1, and coronin [Cell Biology]
Cofilin is an actin filament severing protein necessary for fast actin turnover dynamics. Coronin and Aip1 promote cofilin-mediated actin filament disassembly, but the mechanism is somewhat controversial. An early model proposed that the combination of cofilin, coronin, and Aip1 disassembled filaments in bursts. A subsequent study only reported severing. Here, we used EM to show that actin filaments convert directly into globular material. A monomer trap assay also shows that the combination of all three factors produces actin monomers faster than any two factors alone. We show that coronin accelerates the release of Pi fr...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Vivian W. Tang, Ambika V. Nadkarni, William M. Brieher Tags: Cell Biology Source Type: research

Klp2 and Ase1 synergize to maintain meiotic spindle stability during metaphase I [Cell Biology]
The spindle apparatus segregates bi-oriented sister chromatids during mitosis but mono-oriented homologous chromosomes during meiosis I. It has remained unclear if similar molecular mechanisms operate to regulate spindle dynamics during mitosis and meiosis I. Here, we employed live-cell microscopy to compare the spindle dynamics of mitosis and meiosis I in fission yeast cells and demonstrated that the conserved kinesin-14 motor Klp2 plays a specific role in maintaining metaphase spindle length during meiosis I but not during mitosis. Moreover, the maintenance of metaphase spindle stability during meiosis I requires the syn...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Fan Zheng, Fenfen Dong, Shuo Yu, Tianpeng Li, Yanze Jian, Lingyun Nie, Chuanhai Fu Tags: Cell Biology Source Type: research

Discovery of a heme-binding domain in a neuronal voltage-gated potassium channel [Protein Structure and Folding]
The EAG (ether-à-go-go) family of voltage-gated K+ channels are important regulators of neuronal and cardiac action potential firing (excitability) and have major roles in human diseases such as epilepsy, schizophrenia, cancer, and sudden cardiac death. A defining feature of EAG (Kv10–12) channels is a highly conserved domain on the N terminus, known as the eag domain, consisting of a Per–ARNT–Sim (PAS) domain capped by a short sequence containing an amphipathic helix (Cap domain). The PAS and Cap domains are both vital for the normal function of EAG channels. Using heme-affinity pulldown assays an...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Mark J. Burton, Joel Cresser-Brown, Morgan Thomas, Nicola Portolano, Jaswir Basran, Samuel L. Freeman, Hanna Kwon, Andrew R. Bottrill, Manuel J. Llansola-Portoles, Andrew A. Pascal, Rebekah Jukes-Jones, Tatyana Chernova, Ralf Schmid, Noel W. Davies, Nina Tags: Protein Structure and Folding Source Type: research

Applying gene editing to tailor precise genetic modifications in plants [Plant Biology]
The ability to tailor alterations in genomes, including plant genomes, in a site-specific manner has been greatly advanced through approaches that reduced the complexity and time of genome sequencing along with development of gene editing technologies. These technologies provide a valuable foundation for studies of gene function, metabolic engineering, and trait modification for crop improvement. Development of genome editing methodologies began ∼20 years ago, first with meganucleases and followed by zinc finger nucleases, transcriptional activator-like effector nucleases and, most recently, clustered regulatory inters...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Joyce Van Eck Tags: JBC Reviews Source Type: research

Insulin signaling requires glucose to promote lipid anabolism in adipocytes [Metabolism]
Adipose tissue is essential for metabolic homeostasis, balancing lipid storage and mobilization based on nutritional status. This is coordinated by insulin, which triggers kinase signaling cascades to modulate numerous metabolic proteins, leading to increased glucose uptake and anabolic processes like lipogenesis. Given recent evidence that glucose is dispensable for adipocyte respiration, we sought to test whether glucose is necessary for insulin-stimulated anabolism. Examining lipogenesis in cultured adipocytes, glucose was essential for insulin to stimulate the synthesis of fatty acids and glyceride–glycerol. Impo...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: James R. Krycer, Lake-Ee Quek, Deanne Francis, Armella Zadoorian, Fiona C. Weiss, Kristen C. Cooke, Marin E. Nelson, Alexis Diaz-Vegas, Sean J. Humphrey, Richard Scalzo, Akiyoshi Hirayama, Satsuki Ikeda, Futaba Shoji, Kumi Suzuki, Kevin Huynh, Corey Giles Tags: Metabolism Source Type: research

Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics [Enzymology]
The siderophore biosynthetic enzyme A (SidA) ornithine hydroxylase from Aspergillus fumigatus is a fungal disease drug target involved in the production of hydroxamate-containing siderophores, which are used by the pathogen to sequester iron. SidA is an N-monooxygenase that catalyzes the NADPH-dependent hydroxylation of l-ornithine through a multistep oxidative mechanism, utilizing a C4a-hydroperoxyflavin intermediate. Here we present four new crystal structures of SidA in various redox and ligation states, including the first structure of oxidized SidA without NADP(H) or l-ornithine bound (resting state). The resting stat...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Ashley C. Campbell, Kyle M. Stiers, Julia S. Martin Del Campo, Ritcha Mehra-Chaudhary, Pablo Sobrado, John J. Tanner Tags: Protein Structure and Folding Source Type: research

Complex I mutations synergize to worsen the phenotypic expression of Leber's hereditary optic neuropathy [Molecular Bases of Disease]
In this report, we showed that four Chinese families bearing both m.3866T>C and m.11778G>A mutations exhibited higher penetrances of LHON than 6 Chinese pedigrees carrying only the m.3866T>C mutation or families harboring only the m.11778G>A mutation. The protein structure analysis revealed that the m.3866T>C (I187T) and m.11778G>A (R340H) mutations destabilized the specific interactions with other residues of ND1 and ND4, thereby altering the structure and function of complex I. Cellular data obtained using cybrids, constructed by transferring mitochondria from the Chinese families into mtDNA-less (ρ...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Yanchun Ji, Juanjuan Zhang, Yuanyuan Lu, Qiuzi Yi, Mengquan Chen, Shipeng Xie, Xiaoting Mao, Yun Xiao, Feilong Meng, Minglian Zhang, Rulai Yang, Min-Xin Guan Tags: Bioenergetics Source Type: research

CHOP and c-JUN up-regulate the mutant Z {alpha}1-antitrypsin, exacerbating its aggregation and liver proteotoxicity [Gene Regulation]
α1-Antitrypsin (AAT) encoded by the SERPINA1 gene is an acute-phase protein synthesized in the liver and secreted into the circulation. Its primary role is to protect lung tissue by inhibiting neutrophil elastase. The Z allele of SERPINA1 encodes a mutant AAT, named ATZ, that changes the protein structure and leads to its misfolding and polymerization, which cause endoplasmic reticulum (ER) stress and liver disease through a gain-of-function toxic mechanism. Hepatic retention of ATZ results in deficiency of one of the most important circulating proteinase inhibitors and predisposes to early-onset emphysema through a ...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Sergio Attanasio, Rosa Ferriero, Gwladys Gernoux, Rossella De Cegli, Annamaria Carissimo, Edoardo Nusco, Severo Campione, Jeffrey Teckman, Christian Mueller, Pasquale Piccolo, Nicola Brunetti-Pierri Tags: Molecular Bases of Disease Source Type: research

A new model for Trypanosoma cruzi heme homeostasis depends on modulation of TcHTE protein expression [Metabolism]
Heme is an essential cofactor for many biological processes in aerobic organisms, which can synthesize it de novo through a conserved pathway. Trypanosoma cruzi, the etiological agent of Chagas disease, as well as other trypanosomatids relevant to human health, are heme auxotrophs, meaning they must import it from their mammalian hosts or insect vectors. However, how these species import and regulate heme levels is not fully defined yet. It is known that the membrane protein TcHTE is involved in T. cruzi heme transport, although its specific role remains unclear. In the present work, we studied endogenous TcHTE in the diff...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Lucas Pagura, Evelyn Tevere, Marcelo L. Merli, Julia A. Cricco Tags: Microbiology Source Type: research

Amyloid precursor protein 770 is specifically expressed and released from platelets [Glycobiology and Extracellular Matrices]
In this study, we used peripheral blood samples from patients with CAD and control subjects and evaluated sAPP770 as a specific biomarker for platelet activation. First, the plasma levels of sAPP770 correlated well with those of the soluble form CD40 ligand (CD40L), an established biomarker for platelet activation. Additionally, flow cytometry analysis using peripheral blood cells showed that CD40L expression is up-regulated in activated T cells, whereas APP770 expression is negligible in all blood cell types except platelets. Following stimulation with collagen or ADP, aggregating platelets immediately released sAPP770. F...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Saori Miura, Akiomi Yoshihisa, Tomofumi Misaka, Takayoshi Yamaki, Takao Kojima, Masahiro Toyokawa, Kazuei Ogawa, Hiroki Shimura, Naomasa Yamamoto, Kohji Kasahara, Yasuchika Takeishi, Shinobu Kitazume Tags: Molecular Bases of Disease Source Type: research

The Ca2+ channel CatSper is not activated by cAMP/PKA signaling but directly affected by chemicals used to probe the action of cAMP and PKA [Cell Biology]
The sperm-specific Ca2+ channel CatSper (cation channel of sperm) controls the influx of Ca2+ into the flagellum and, thereby, the swimming behavior of sperm. A hallmark of human CatSper is its polymodal activation by membrane voltage, intracellular pH, and oviductal hormones. Whether CatSper is also activated by signaling pathways involving an increase of cAMP and ensuing activation of PKA is, however, a matter of controversy. To shed light on this question, we used kinetic ion-sensitive fluorometry, patch-clamp recordings, and optochemistry to study transmembrane Ca2+ flux and membrane currents in human sperm from health...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Tao Wang, Samuel Young, Henrike Krenz, Frank Tuttelmann, Albrecht Ropke, Claudia Krallmann, Sabine Kliesch, Xu–Hui Zeng, Christoph Brenker, Timo Strunker Tags: Signal Transduction Source Type: research

Angiotensin II type 1 receptor variants alter endosomal receptor-{beta}-arrestin complex stability and MAPK activation [Signal Transduction]
The angiotensin II (AngII) type 1 receptor (AT1R), a member of the G protein–coupled receptor (GPCR) family, signals through G proteins and β-arrestins, which act as adaptors to regulate AT1R internalization and mitogen-activated protein kinase (MAPK) ERK1/2 activation. β-arrestin–dependent ERK1/2 regulation is the subject of important studies because its spatiotemporal control remains poorly understood for many GPCRs, including AT1R. To study the link between β-arrestin–dependent trafficking and ERK1/2 signaling, we investigated three naturally occurring AT1R variants that show distinct re...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Yubo Cao, Sahil Kumar, Yoon Namkung, Laurence Gagnon, Aaron Cho, Stephane A. Laporte Tags: Cell Biology Source Type: research

H2S and reactive sulfur signaling at the host-bacterial pathogen interface [Gene Regulation]
Bacterial pathogens that cause invasive disease in the vertebrate host must adapt to host efforts to cripple their viability. Major host insults are reactive oxygen and reactive nitrogen species as well as cellular stress induced by antibiotics. Hydrogen sulfide (H2S) is emerging as an important player in cytoprotection against these stressors, which may well be attributed to downstream more oxidized sulfur species termed reactive sulfur species (RSS). In this review, we summarize recent work that suggests that H2S/RSS impacts bacterial survival in infected cells and animals. We discuss the mechanisms of biogenesis and cle...
Source: Journal of Biological Chemistry - September 18, 2020 Category: Chemistry Authors: Brenna J. C. Walsh, David P. Giedroc Tags: JBC Reviews Source Type: research