Mechanism and kinetics of a sodium-driven bacterial flagellar motor
Chien-Jung Lo, Yoshiyuki Sowa, Teuta Pilizota, and Richard M. Berry
Using new experimental methods, we measure the mechanical output of the bacterial flagellar motor, the rotary molecular machine that propels swimming bacteria, while varying both electrical and chemical components of the ion-motive force that drives it. We find (pp. E2544–E2551) that each independent torque-generating stator in the motor passes 37 ± 2 ions per revolution, at odds with previous indications of 26 or 52 ions. Fitting our data to theoretical models reveals the kinetics of the motor mechanism. Our thorough search of the multidimensional parameter space of generalized motor models, guided by experimental data, is an approach that may be widely applicable.
Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site
Paul A. Sigala, Aaron T. Fafarman, Jason P. Schwans, Stephen D. Fried, Timothy D. Fenn, Jose M. M. Caaveiro, Brandon Pybus, Dagmar Ringe, Gregory A. Petsko, Steven G. Boxer, and Daniel Herschlag
Hydrogen bond networks play critical structural and functional roles in proteins but have been challenging to study within this complex environment. We incorporated spectroscopic probes into the active site of the bacterial enzyme ketosteroid isomerase to systematically dissect the proton transfer equilibrium within a key hydrogen bond network formed to bound transition state analogs. Our study (pp. E2552–E2561) provides direct insight into the physical and energetic properties of a hydrogen bond network within an enzyme and presents a simple computational model of electrostatic effects within this protein that succeeds due to detailed knowledge of ionization states and a tightly controlled experimental system.
On the mechanism of recombination hotspot scanning during double-stranded DNA break resection
Carolina Carrasco, Neville S. Gilhooly, Mark S. Dillingham, and Fernando Moreno-Herrero
We report the use of the magnetic tweezers approach to monitor the dynamics of double-stranded DNA break resection at single-molecule resolution. In this work (pp. E2562–E2571), we unveil the inner workings of the Bacillus subtilis AddAB complex by showing that the domain responsible for the recognition of the recombination hotspot sequence Crossover hotspot instigator (Chi) antagonizes the translocation activity, causing the complex to transiently stall at Chi and Chi-like sequences. We propose a simple model for failed and successful Chi recognition in which the battle between the translocation and sequence-specific binding activities acts as a selectivity filter for bona fide Chi sequences.
Molecular circuit involving KLK4 integrates androgen and mTOR signaling in prostate cancer
Yang Jin, Su Qu, Martina Tesikova, Ling Wang, Alexandr Kristian, Gunhild M. Mælandsmo, Haiying Kong, Tianzhou Zhang, Carmen Jerónimo, Manuel R. Teixeira, Erkan Yuca, Ibrahim Tekedereli, Kivanc Gorgulu, Neslihan Alpay, Anil K. Sood, Gabriel Lopez-Berestein, Håvard E. Danielsen, Bulent Ozpolat, and Fahri Saatcioglu
All cancer lesions sustain alterations in signaling pathways, which are the drivers of disease initiation and progression. Study of altered signaling in cancer is thus important to develop more effective therapeutic regimens as well as better prognostic markers. In this study, we show that two of the most frequently altered signaling pathways in prostate cancer, the androgen receptor and the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin pathways, are dependent on kallikrein related peptidase 4 (KLK4), whose expression is highly prostate enriched. Our results (pp. E2572–E2581) suggest that KLK4 has a central role in prostate cancer survival and that KLK4 silencing may have significant therapeutic efficacy.
Decorin causes autophagy in endothelial cells via Peg3
Simone Buraschi, Thomas Neill, Atul Goyal, Chiara Poluzzi, James Smythies, Rick T. Owens, Liliana Schaefer, Annabel Torres, and Renato V. Iozzo
We identified a function for a member of the extracellular matrix in the regulation of autophagy. Decorin, a member of the small leucine-rich proteoglycan family and an established pan-receptor tyrosine kinase inhibitor, evokes endothelial cell autophagy and inhibits angiogenesis. This process is mediated by a high-affinity interaction with VEGFR2 which leads to increased levels of Peg3, a tumor-suppressor gene. We provide mechanistic evidence that Peg3 is required to maintain basal levels of Beclin 1, a major autophagic marker. These data (pp. E2582–E2591) provide a paradigmatic shift for other soluble matrix constituents to regulate autophagy.
Histone deacetylase 10 promotes autophagy-mediated cell survival
Ina Oehme, Jan-Peter Linke, Barbara C. Böck, Till Milde, Marco Lodrini, Bettina Hartenstein, Inga Wiegand, Christian Eckert, Wilfried Roth, Marcel Kool, Sylvia Kaden, Hermann-Josef Gröne, Johannes H. Schulte, Sven Lindner, Anne Hamacher-Brady, Nathan R. Brady, Hedwig E. Deubzer, and Olaf Witt
Resistance to chemotherapy is one of the major challenges in oncology. Neuroblastoma is the most common extracranial solid tumor in childhood, and the successful response of high-risk patients to chemotherapy remains poor. Our work (pp. E2592–E2601) showed that the so far poorly studied histone deacetylase (HDAC)10 promotes autophagy-mediated cell survival and signals poor outcome in independent high-risk patient cohorts. Inhibition of HDAC10 sensitized tumor cells for cytotoxic drug treatment. These results offer HDAC10 as a potential biomarker for treatment response of high-risk tumors and open new avenues for developing selective treatment strategies to bypass drug resistance of these tumors.
Global patterns of terrestrial vertebrate diversity and conservation
Clinton N. Jenkins, Stuart L. Pimm, and Lucas N. Joppa
Identifying priority areas for biodiversity is essential for directing conservation resources. We mapped global priority areas using the latest data on mammals, amphibians, and birds at a scale 100 times finer than previous assessments. Priority areas have a higher—but still insufficient—rate of protection than the global average. We identify several important areas currently ignored by biodiversity hotspots, the current leading priority map. As the window of opportunity for expanding the global protected area network begins to close, identifying priorities at a scale practical for local action ensures our findings (pp. E2602–E2610) will help protect biodiversity most effectively.
MS/MS networking guided analysis of molecule and gene cluster families
Don Duy Nguyen, Cheng-Hsuan Wu, Wilna J. Moree, Anne Lamsa, Marnix H. Medema, Xiling Zhao, Ronnie G. Gavilan, Marystella Aparicio, Librada Atencio, Chanaye Jackson, Javier Ballesteros, Joel Sanchez, Jeramie D. Watrous, Vanessa V. Phelan, Corine van de Wiel, Roland D. Kersten, Samina Mehnaz, René De Mot, Elizabeth A. Shank, Pep Charusanti, Harish Nagarajan, Brendan M. Duggan, Bradley S. Moore, Nuno Bandeira, Bernhard Ø. Palsson, Kit Pogliano, Marcelino Gutiérrez, and Pieter C. Dorrestein
The paper introduces the concepts of molecular families (MFs) and gene cluster families (GCFs). We define MFs as structurally related molecules based on their mass spectral fragmentation patterns, whereas GCFs are biosynthetic gene clusters that show similar gene cluster organization with a high degree of sequence similarity. We use (pp. E2611–E2620) MS/MS networking as a tool to map the molecular network of more than 60 organisms, most of which are unsequenced, and locate their nonribosomal peptide MFs. These MFs from unsequenced organisms are then connected to GCFs of publicly available genome sequences of closely related organisms.
Modulation of reactivation of latent herpes simplex virus 1 in ganglionic organ cultures by p300/CBP and STAT3
Te Du, Guoying Zhou, and Bernard Roizman
HSVs initiate human infections with the aid of viral tegument proteins brought along with viral DNA into cells. These viruses then enter and establish latent, silent infection in sensory ganglia. Periodically, HSV reactivates from a latent state. A key unresolved question (pp. E2621–E2628) is the mechanism by which the virus reactivates in the absence of the tegument proteins. Studies of murine trigeminal ganglia harboring latent virus and maintained in organ cultures suggest that viral DNA is maintained in a dynamic equilibrium favoring gene repression. The equilibrium shifts toward gene expression on inactivation of histone deacetylases, inhibition of STAT3, or activation of p300/CBP.
Permeation rates of penicillins indicate that Escherichia coli porins function principally as nonspecific channels
Seiji Kojima and Hiroshi Nikaido
Porin channels in the outer membrane of Gram-negative bacteria were originally thought to be nonspecific channels that discriminate among solutes only by their gross physicochemical properties, such as size, hydrophobicity, and charge. Since the discovery of the ampicillin-binding site inside one porin channel, however, such “specific” interactions are hypothesized to play significant roles especially for the permeation of drugs. We show (pp. E2629–E2634), by the careful examination of influx and efflux of ampicillin and benzylpenicillin, that the original nonspecific model is still valid and that it is misleading to overemphasize the role of specific binding sites.
Transformation of the neural code for tactile detection from thalamus to cortex
Yuriria Vázquez, Emilio Salinas, and Ranulfo Romo
Place a hand on the hood of a car and ask, is it running or not? Answering this involves the sequential activation of many neurons, from mechanoreceptors under the skin to cortical neurons whose activity is closely related to the evoked internal sensation. We investigate how vibratory stimuli are represented in two steps along this processing chain during a detection task. We find (pp. E2635–E2644) that activity changes from a “literal” code, in which neural responses faithfully track the stimulus, to a more abstract and robust one, from which other neurons can more easily infer whether a stimulus was presented or not.
Correlations in ion channel expression emerge from homeostatic tuning rules
Timothy O'Leary, Alex H. Williams, Jonathan S. Caplan, and Eve Marder
A deep puzzle in neuroscience is how neurons maintain their electrical properties despite continuous ion channel turnover and activity perturbations. Previous work proposed that activity-dependent homeostatic rules ensure robust development of excitability by regulating channel density, although it is not understood how these rules shape the distribution of ion channel types nor how finely tuned these rules must be. We show (pp. E2645–E2654) that generic homeostatic regulation rules impose correlations in the steady-state distribution of ion channels, as has been recently observed experimentally. Specific correlations depend on relative expression rates, and the regulation rules themselves are far more robust than previously thought.
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
Daniel Koenig, José M. Jiménez-Gómez, Seisuke Kimura, Daniel Fulop, Daniel H. Chitwood, Lauren R. Headland, Ravi Kumar, Michael F. Covington, Upendra Kumar Devisetty, An V. Tat, Takayuki Tohge, Anthony Bolger, Korbinian Schneeberger, Stephan Ossowski, Christa Lanz, Guangyan Xiong, Mallorie Taylor-Teeples, Siobhan M. Brady, Markus Pauly, Detlef Weigel, Björn Usadel, Alisdair R. Fernie, Jie Peng, Neelima R. Sinha, and Julin N. Maloof
One of the most important technological advances by humans is the domestication of plant species for the production of food. We have used high-throughput sequencing to identify changes in DNA sequence and gene expression that differentiate cultivated tomato and its wild relatives. We also identify hundreds of candidate genes that have evolved new protein sequences or have changed expression levels in response to natural selection in wild tomato relatives. Taken together, our analyses (pp. E2655–E2662) provide a snapshot of genome evolution under artificial and natural conditions.