Active sites and mechanisms for H2O2 decomposition over Pd catalysts
Anthony Plauck, Eric E. Stangland, James A. Dumesic, and Manos Mavrikakis
The use of hydrogen peroxide (H2O2) for catalytic oxidations is limited by the energy-intensive and wasteful process by which H2O2 is currently produced—the anthraquinone process. The direct synthesis of H2O2 (DSHP) is a promising alternative process, yet catalysts active for this reaction (Pd being the most widely studied) are generally hindered by subsequent H2O2 decomposition. Through a combined theoretical and experimental approach, our work (i) provides an understanding of the nature of Pd active sites responsible for H2O2 decomposition and (ii) identifies a single type of elementary step that controls the rate. These structural and mechanistic insights are important for designing improved DSHP catalysts and for developing transition-metal–catalyzed oxidations that efficiently use H2O2. (See pp. E1973–E1982.)
Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis
Lin Bai, Kuan Hu, Tong Wang, Jordan M. Jastrab, K. Heran Darwin, and Huilin Li
Mycobacterium tuberculosis (Mtb) has evolved a sophisticated toolkit to cope with the harsh environment inside its natural host, the human macrophage. Macrophages are immune cells that normally kill invading microbes; however, Mtb has a proteasome system that allows it to persist and cause lethal infections in animals. Although the Mtb proteasome core particle is evolutionally related to its eukaryotic counterpart, factors involved in targeting doomed proteins to the mycobacterial proteasome appear to be distinct. A prime example is the bacterial pupylation pathway, which is biochemically unrelated to the eukaryotic ubiquitylation system. Here, we describe a second example: a bacterial proteasome activator called PafE (Rv3780), which is structurally unlike any previously characterized proteasome activator in biology. (See pp. E1983–E1992.)
Photochemical reaction cycle transitions during anion channelrhodopsin gating
Oleg A. Sineshchekov, Hai Li, Elena G. Govorunova, and John L. Spudich
The discovery of natural anion channelrhodopsins (ACRs) opens possibilities for rapid and efficient inhibition of neuronal firing by hyperpolarization, but molecular mechanisms of these proteins’ function remain elusive. We studied spectral properties and photochemical conversions of purified wild-type and mutant ACRs to probe the coupling between chromophore photoexcitation and alteration of protein conformation leading to electrical conductance in the membrane. Our results show that not only the selectivity filter, but also the structural basis of channel gating in the cryptophyte ACRs differs from that in cation channelrhodopsins (CCRs) from chlorophyte algae used to depolarize the membrane. The knowledge of structure–function relationships in ACRs will benefit molecular engineering to improve their performance as tools for optogenetic research and therapies. (See pp. E1993–E2000.)
Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles
Olivier Julien, Min Zhuang, Arun P. Wiita, Anthony J. O’Donoghue, Giselle M. Knudsen, Charles S. Craik, and James A. Wells
Caspases, a family of 12 proteases involved in irreversible cell state changes including cell death, often cleave common substrates. However, we show here by quantitative N-terminomics MS, for caspase-2 and caspase-6, that the rates of substrate cleavage vary more than 500-fold in cellular lysate. The rates of cleavage show virtually no correlation among common substrates for these two caspases, as well as for three other caspases previously studied: caspase-3, caspase-7, and caspase-8. These global and unbiased studies reveal a greater degree of substrate hierarchy and specialized functions for caspases than previously appreciated. We believe this quantitative approach is of general use to other proteases and enzymes involved in posttranslational modifications to better define their roles. (See pp. E2001–E2010.)
Suramin inhibits cullin-RING E3 ubiquitin ligases
Kenneth Wu, Robert A. Chong, Qing Yu, Jin Bai, Donald E. Spratt, Kevin Ching, Chan Lee, Haibin Miao, Inger Tappin, Jerard Hurwitz, Ning Zheng, Gary S. Shaw, Yi Sun, Dan P. Felsenfeld, Roberto Sanchez, Jun-nian Zheng, and Zhen-Qiang Pan
Interactions between E2 and E3 enzymes are key for ubiquitination, but whether such a dynamic association is susceptible to perturbation by small-molecule modulators remains elusive. By demonstrating that suramin can inhibit cullin-RING E3 ubiquitin ligase by disrupting its ability to recruit E2 Cdc34, this work suggests that the E2–E3 interface may be druggable. In addition, suramin is an antitrypansomal drug that also possesses antitumor activity. Our findings have linked the ubiquitin-proteasome pathway to suramin and suggest additional biochemical mode of action for this century-old drug. (See pp. E2011–E2018.)
Spatial landmarks regulate a Cdc42-dependent MAPK pathway to control differentiation and the response to positional compromise
Sukanya Basu, Nadia Vadaie, Aditi Prabhakar, Boyang Li, Hema Adhikari, Andrew Pitoniak, Jacky Chow, Colin A. Chavel, and Paul J. Cullen
We identify a new role for bud-site–selection proteins outside of their established roles in regulating growth site determination, as components of a surveillance pathway that monitors spatial position during intrinsic and extrinsic morphogenetic stress and regulates a Cdc42p- and MAPK-dependent response. (See pp. E2019–E2028.)
Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X
Jianle Wang, Camille M. Syrett, Marianne C. Kramer, Arindam Basu, Michael L. Atchison, and Montserrat C. Anguera
Females have increased immune responsiveness than males, and they are more likely to develop autoimmune disorders. The mechanism underlying these observations is unclear, and hypotheses suggest an important role for the X chromosome. Here, we discover that the inactive X is predisposed to become partially reactivated in mammalian female lymphocytes, resulting in the overexpression of immunity-related genes. We also demonstrate that lymphocytes from systemic lupus erythematosus patients have different epigenetic characteristics on the inactive X that compromises transcriptional silencing. These findings are the first to our knowledge to link the unusual maintenance of X chromosome Inactivation (the female-specific mechanism for dosage compensation) in lymphocytes to the female bias observed with enhanced immunity and autoimmunity susceptibility. (See pp. E2029–E2038.)
Regulation of normal B-cell differentiation and malignant B-cell survival by OCT2
Daniel J. Hodson, Arthur L. Shaffer, Wenming Xiao, George W. Wright, Roland Schmitz, James D. Phelan, Yandan Yang, Daniel E. Webster, Lixin Rui, Holger Kohlhammer, Masao Nakagawa, Thomas A. Waldmann, and Louis M. Staudt
Diffuse large B-cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma and is incurable in roughly 30% of cases. Here we demonstrate the addiction of both major subtypes of DLBCL to the expression of the transcription factor OCT2 (octamer-binding protein 2) and its co-activator OCA-B. We clarify the role of OCT2 in normal germinal center biology and identify the genes and pathways that it regulates in malignant B cells. Our findings suggest that pharmacological agents designed to target OCT2 itself or the OCT2–OCA-B interface would be an effective and nontoxic therapeutic strategy in DLBCL. (See pp. E2039–E2046.)
Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA
Chuanzhao Zhang, Debangshu Samanta, Haiquan Lu, John W. Bullen, Huimin Zhang, Ivan Chen, Xiaoshun He, and Gregg L. Semenza
Pluripotency factors, such as NANOG, play a critical role in the maintenance and specification of cancer stem cells, which are required for primary tumor formation and metastasis. In this study, we report that exposure of breast cancer cells to hypoxia (i.e., reduced O2 availability), which is a critical feature of the tumor microenvironment, induces N6-methyladenosine (m6A) demethylation and stabilization of NANOG mRNA, thereby promoting the breast cancer stem cell (BCSC) phenotype. We show that inhibiting the expression of AlkB homolog 5 (ALKBH5), which demethylates m6A, or the hypoxia-inducible factors (HIFs) HIF-1α and HIF-2α, which activate ALKBH5 gene transcription in hypoxic breast cancer cells, is an effective strategy to decrease NANOG expression and target BCSCs in vivo. (See pp. E2047–E2056.)
Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development
Haruna Takeda, Alistair G. Rust, Jerrold M. Ward, Christopher Chin Kuan Yew, Nancy A. Jenkins, and Neal G. Copeland
Gastric cancer is the third leading cause of cancer mortality, with an overall 5-y survival rate of <25%. Although sequencing and comprehensive molecular profiling of human gastric cancer have identified a wide spectrum of genes that drive gastric cancer development, we are still far from understanding the complete pathophysiology of this disease. Here, we used Sleeping Beauty transposon mutagenesis to identify genes and evolutionary forces driving gastric cancer development. This study identified pathways driving gastric cancer development, including WNT, TGF-β, PI3K signaling, ubiquitin-mediated proteolysis, adherens junctions, RNA degradation, and chromatin modification, and discovered many previously unidentified genes, such as the LDL receptor-related protein 1B (LRP1B) tumor suppressor gene, with potential clinical importance in human gastric cancer. (See pp. E2057–E2065.)
Architectural transitions in Vibrio cholerae biofilms at single-cell resolution
Knut Drescher, Jörn Dunkel, Carey D. Nadell, Sven van Teeffelen, Ivan Grnja, Ned S. Wingreen, Howard A. Stone, and Bonnie L. Bassler
Bacterial biofilms are ubiquitous in the environment and serve beneficial roles in microbiota communities in the context of eukaryotic hosts and in industrial applications, yet biofilms of pathogenic bacteria can also cause devastating infections. Biofilm architectures are usually studied at a coarse morphological level, and consequently, little is known about the internal biofilm architecture and how it emerges. Here, we use an optical imaging technique to visualize every cell inside thousands of Vibrio cholerae biofilms to discover architectural transitions and the major phases of V. cholerae biofilm growth. (See pp. E2066–E2072.)
Functional identification of a neurocircuit regulating blood glucose
Thomas H. Meek, Jarrell T. Nelson, Miles E. Matsen, Mauricio D. Dorfman, Stephan J. Guyenet, Vincent Damian, Margaret B. Allison, Jarrad M. Scarlett, Hong T. Nguyen, Joshua P. Thaler, David P. Olson, Martin G. Myers Jr., Michael W. Schwartz, and Gregory J. Morton
Hypoglycemia is an important and frequently encountered complication of diabetes treatment. Here, we identify a subset of neurons located in the ventromedial hypothalamic nucleus, activation of which is both necessary and sufficient to mediate adaptive counterregulatory responses to hypoglycemia that return low blood glucose levels into the normal range. These neurons receive ascending input from neurons in the lateral parabrachial nucleus and in turn control blood glucose levels via projections to the anterior bed nucleus of the stria terminalis. Together, this work identifies a previously unrecognized functional neurocircuit involved in glycemic control. (See pp. E2073–E2082.)
Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids
Mélanie Rigal, Claude Becker, Thierry Pélissier, Romain Pogorelcnik, Jane Devos, Yoko Ikeda, Detlef Weigel, and Olivier Mathieu
Similar to changes in DNA sequence, induced or naturally occurring variation in cytosine methylation can impact gene expression. How distinct methylation states of genes and transposons, called epialleles, emerge is not well understood. Here, we report that combining identical genomes with drastically different DNA methylation patterns in the same individual results in an epigenomic shock that is characterized by widespread changes in DNA methylation and gene expression. Many novel epialleles not found in the parents are formed at genes whereas transposons often experience decreased DNA methylation associated with transcriptional activation. Our work provides a scenario for the rapid and broad-scale emergence of epigenetic variation and may have implications for transposon dynamics within populations. (See pp. E2083–E2092.)