Evolutionary alteration of ALOX15 specificity optimizes the biosynthesis of antiinflammatory and proresolving lipoxins
Susan Adel, Felix Karst, Àngels González-Lafont, Mária Pekárová, Patricia Saura, Laura Masgrau, José M. Lluch, Sabine Stehling, Thomas Horn, Hartmut Kuhn, and Dagmar Heydeck
Lipoxygenases are lipid-peroxidizing enzymes that have been classified according to their reaction specificity. ALOX15 (12/15-lipoxygenase) has been implicated in inflammatory resolution via biosynthesis of antiinflammatory and proresolving lipoxins. We found that lower mammals including lower primates express arachidonic acid 12-lipoxygenating ALOX15 orthologs, whereas higher primates express 15-lipoxygenating enzymes. Gibbons constitute the missing link interconnecting 12- and 15-lipoxygenating ALOX15 orthologs. To explore the evolutionary driving force for this specificity alteration, we quantified the lipoxin synthase activity of 12- and 15-lipoxygenating ALOX15 orthologs and observed that the lipoxin synthase activities of 15-lipoxygenating enzymes were significantly higher. These results suggest an evolution of ALOX15 specificity, which optimizes the biosynthetic capacity for antiinflammatory and proresolving lipoxins. (See pp. E4266–E4275.)
Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria
Gokhan Akman, Radha Desai, Laura J. Bailey, Takehiro Yasukawa, Ilaria Dalla Rosa, Romina Durigon, J. Bradley Holmes, Chloe F. Moss, Mara Mennuni, Henry Houlden, Robert J. Crouch, Michael G. Hanna, Robert D. S. Pitceathly, Antonella Spinazzola, and Ian J. Holt
The DNA in mitochondria is essential for efficient energy production. Critical for mitochondrial DNA replication and expression are sequences concentrated in the so-called control region. We report that many mitochondrial DNAs contain a triple-stranded region whose third strand is RNA and maps to the control region. These R-loops contribute to DNA architecture and replication in the mitochondria, and aberrant R-loop processing causes disease. (See pp. E4276–E4285.)
Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds
Dzmitry Padhorny, Andrey Kazennov, Brandon S. Zerbe, Kathryn A. Porter, Bing Xia, Scott E. Mottarella, Yaroslav Kholodov, David W. Ritchie, Sandor Vajda, and Dima Kozakov
Expressing the interaction energy as sum of correlation functions, fast Fourier transform (FFT) based methods speed the calculation, enabling the sampling of billions of putative protein–protein complex conformations. However, such acceleration is currently achieved only on a 3D subspace of the full 6D rotational/translational space, and the remaining dimensions must be sampled using conventional slow calculations. Here we present an algorithm that employs FFT-based sampling on the 5D rotational space, and only the 1D translations are sampled conventionally. The accuracy of the results is the same as those of earlier methods, but the calculation is an order of magnitude faster. Also, it is inexpensive computationally to add more correlation function terms to the scoring function compared with classical approaches. (See pp. E4286–E4293.)
Cell division plane orientation based on tensile stress in Arabidopsis thaliana
Marion Louveaux, Jean-Daniel Julien, Vincent Mirabet, Arezki Boudaoud, and Olivier Hamant
The control of cell division plane orientation is crucial in biology and most particularly in plants, in which cells cannot rearrange their positions, as they are glued to each other by their cell walls. Cell geometry has long been proposed to determine cell division plane orientation. Here, using statistical analysis, modeling, and live imaging in the Arabidopsis shoot apex, we show that plant cells instead divide along maximal tension. (See pp. E4294–E4303.)
Minimal basilar membrane motion in low-frequency hearing
Rebecca L. Warren, Sripriya Ramamoorthy, Nikola Ciganović, Yuan Zhang, Teresa M. Wilson, Tracy Petrie, Ruikang K. Wang, Steven L. Jacques, Tobias Reichenbach, Alfred L. Nuttall, and Anders Fridberger
To perceive speech, the brain relies on inputs from sensory cells located near the top of the spiral-shaped cochlea. This low-frequency region of the inner ear is anatomically difficult to access, and it has not previously been possible to study its mechanical response to sound in intact preparations. Here, we used optical coherence tomography to image sound-evoked vibration inside the intact cochlea. We show that low-frequency sound moves a small portion of the basilar membrane, and that the motion declines in an exponential manner across the basilar membrane. Hence, the response of the hearing organ to speech-frequency sounds is different from the one evident in high-frequency cochlear regions. (See pp. E4304–E4310.)
DNA damage tolerance pathway involving DNA polymerase ι and the tumor suppressor p53 regulates DNA replication fork progression
Stephanie Hampp, Tina Kiessling, Kerstin Buechle, Sabrina F. Mansilla, Jürgen Thomale, Melanie Rall, Jinwoo Ahn, Helmut Pospiech, Vanesa Gottifredi, and Lisa Wiesmüller
DNA damage tolerance pathways like translesion synthesis and recombination facilitate the bypass of replication-blocking lesions. Such events are crucial for the survival of rapidly proliferating cells, including cancer and stem cells undergoing active duplication during tissue renewal. Herein, we characterize an unprecedented damage tolerance pathway that requires the combined function of a highly enigmatic translesion DNA polymerase ι (POLι) and the so-called guardian-of-the-genome, p53. We provide evidence demonstrating that p53 complexed with POLι triggers idling events that decelerate nascent DNA elongation at replication barriers, facilitating the resolution of stalled forks by specialized structure-specific enzymes. Our findings implicate p53 in the protection of quickly growing cancer and stem cells from endogenous and exogenous sources of replication stress. (See pp. E4311–E4319.)
Vimentin coordinates fibroblast proliferation and keratinocyte differentiation in wound healing via TGF-β–Slug signaling
Fang Cheng, Yue Shen, Ponnuswamy Mohanasundaram, Michelle Lindström, Johanna Ivaska, Tor Ny, and John E. Eriksson
The central concept in this study is that a major cytoskeletal component, vimentin, acts as a signal integrator during wound healing, operating in both signal-triggering and signal-receiving cells. This is a previously unreported concept for intermediate filaments, with an evolving paradigm according to which intermediate filaments emerge as integrators of regeneration with specific functions in the particular tissues for which individual intermediate filaments are characteristic. Our study reveals the underlying molecular and cellular control functions of vimentin in vimentin-dependent epithelial–mesenchymal transition, regeneration, and healing. (See pp. E4320–E4327.)
AKAP220 manages apical actin networks that coordinate aquaporin-2 location and renal water reabsorption
Jennifer L. Whiting, Leah Ogier, Katherine A. Forbush, Paula Bucko, Janani Gopalan, Ole-Morten Seternes, Lorene K. Langeberg, and John D. Scott
Systemic control of water homeostasis is a vital physiological process. Vasopressin-regulated reabsorption of water through aquaporin-2 (AQP2) water pores in the kidney preserves fluid balance and results in more concentrated urine. We have discovered that the scaffolding protein A-Kinase Anchoring Protein 220 (AKAP220) controls vasopressin-independent aspects of AQP2 trafficking at apical membranes of cells of the kidney-collecting ducts. We postulate that this proceeds via a molecular mechanism that evokes RhoA-mediated modulation of “actin barrier” dynamics. Loss of AKAP220 leads to accumulation of AQP2 at the apical plasma membrane and reduces urine-diluting capacity during overhydration. This phenotype may be clinically relevant, as accumulation of AQP2 at the apical membrane is the desired therapeutic outcome when treating patients with certain renal disorders, including nephrogenic diabetes insipidus. (See pp. E4328–E4337.)
Phosphoinositide 3-kinase inhibitors induce DNA damage through nucleoside depletion
Ashish Juvekar, Hai Hu, Sina Yadegarynia, Costas A. Lyssiotis, Soumya Ullas, Evan C. Lien, Gary Bellinger, Jaekyoung Son, Rosanna C. Hok, Pankaj Seth, Michele B. Daly, Baek Kim, Ralph Scully, John M. Asara, Lewis C. Cantley, and Gerburg M. Wulf
Mutations in the PI3K pathway are highly prevalent in cancers, and isoform-specific and pan-PI3K inhibitors have entered clinical trials in both solid and hematologic malignancies. The PI3K δ-specific inhibitor idelalisib (in combination with rituximab) was recently approved for the treatment of chronic lymphocytic leukemia. However, identifying tumor types and biological mechanisms that predict for response to PI3K inhibitors as single agents or in combination has been a challenge. Our data indicate that PI3K inhibitors induce DNA damage in tumors that have defects in DNA damage-repair pathways and that they do so by impairing the production of Rib phosphate and amino acids needed for deoxynucleotide synthesis. (See pp. E4338–E4347.)
The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501
Yuhua Zhan, Yongliang Yan, Zhiping Deng, Ming Chen, Wei Lu, Chao Lu, Liguo Shang, Zhimin Yang, Wei Zhang, Wei Wang, Yun Li, Qi Ke, Jiasi Lu, Yuquan Xu, Liwen Zhang, Zhihong Xie, Qi Cheng, Claudine Elmerich, and Min Lin
The biological nitrogen fixation process responsible for the reduction of atmospheric nitrogen to ammonia represents the primary source of nitrogen supporting extant life. We have identified a novel noncoding RNA (ncRNA) in the Pseudomonas stutzeri core genome, called NfiS, that is involved in the stress response and controls the expression of genes located in a genomic nitrogen-fixing (nif) island. NfiS was found to optimize nitrogen fixation by the direct posttranscriptional regulation of nitrogenase gene nifK mRNA. The acquisition of the nif island and the recruitment of NfiS by nifK mRNA are evolutionary events that seem to contribute to fine-tuned regulation of nitrogenase activity in P. stutzeri. This study provides a new regulatory pathway, mediated by an ncRNA for optimal nitrogen fixation, that may operate in other diazotrophs. (See pp. E4348–E4356.)
Structural model of the dimeric Parkinson’s protein LRRK2 reveals a compact architecture involving distant interdomain contacts
Giambattista Guaitoli, Francesco Raimondi, Bernd K. Gilsbach, Yacob Gómez-Llorente, Egon Deyaert, Fabiana Renzi, Xianting Li, Adam Schaffner, Pravin Kumar Ankush Jagtap, Karsten Boldt, Felix von Zweydorf, Katja Gotthardt, Donald D. Lorimer, Zhenyu Yue, Alex Burgin, Nebojsa Janjic, Michael Sattler, Wim Versées, Marius Ueffing, Iban Ubarretxena-Belandia, Arjan Kortholt, and Christian Johannes Gloeckner
Leucine-rich repeat kinase 2 (LRRK2) represents a promising drug target for treatment and prevention of Parkinson’s disease (PD), because mutations in LRRK2 are the most common cause of Mendelian forms of the disease. PD-associated LRRK2 variants show decreased GTPase and increased kinase activity. By integrating multiple experimental inputs provided by chemical cross-linking, small-angle X-ray scattering, and a negative-stain EM map, we present, to our knowledge, the first structural model of the full-length LRRK2 dimer. The model reveals a compact folding of the LRRK2 dimer with multiple domain–domain interactions that might be involved in the regulation of LRRK2 enzymatic properties. (See pp. E4357–E4366.)
Disruptions of network connectivity predict impairment in multiple behavioral domains after stroke
Joshua Sarfaty Siegel, Lenny E. Ramsey, Abraham Z. Snyder, Nicholas V. Metcalf, Ravi V. Chacko, Kilian Weinberger, Antonello Baldassarre, Carl D. Hacker, Gordon L. Shulman, and Maurizio Corbetta
Since the early days of neuroscience, the relative merit of structural vs. functional network accounts in explaining neurological deficits has been intensely debated. Using a large stroke cohort and a machine-learning approach, we show that visual memory and verbal memory deficits are better predicted by functional connectivity than by lesion location, and visual and motor deficits are better predicted by lesion location than functional connectivity. In addition, we show that disruption to a subset of cortical areas predicts general cognitive deficit (spanning multiple behavior domains). These results shed light on the complementary value of structural vs. functional accounts of stroke, and provide a physiological mechanism for general multidomain deficits seen after stroke. (See pp. E4367–E4376.)
Decreased function of survival motor neuron protein impairs endocytic pathways
Maria Dimitriadi, Aaron Derdowski, Geetika Kalloo, Melissa S. Maginnis, Patrick O’Hern, Bryn Bliska, Altar Sorkaç, Ken C. Q. Nguyen, Steven J. Cook, George Poulogiannis, Walter J. Atwood, David H. Hall, and Anne C. Hart
Spinal muscular atrophy (SMA) is a devastating motor neuron disease, caused by decreased levels of the ubiquitous survival motor neuron (SMN) protein. Despite the well-characterized role of SMN in pre-mRNA splicing, it remains unclear why SMA has a high carrier frequency (∼1:50 Caucasians) and why diminished SMN affects synaptic function. Here, we demonstrate for the first time, to our knowledge, that SMN depletion causes defects in endosomal trafficking that impair synaptic function. Additionally, diminished SMN in human cells reduced endocytosis-dependent viral infection. It is possible that decreased SMN function may increase resistance to infection. Our findings point to endocytic trafficking as a major player in SMA pathogenesis. (See pp. E4377–E4386.)
Lmx1a and Lmx1b regulate mitochondrial functions and survival of adult midbrain dopaminergic neurons
Hélène Doucet-Beaupré, Catherine Gilbert, Marcos Schaan Profes, Audrey Chabrat, Consiglia Pacelli, Nicolas Giguère, Véronique Rioux, Julien Charest, Qiaolin Deng, Ariadna Laguna, Johan Ericson, Thomas Perlmann, Siew-Lan Ang, Francesca Cicchetti, Martin Parent, Louis-Eric Trudeau, and Martin Lévesque
Degeneration of midbrain dopamine neurons is the main pathological hallmark of Parkinson’s disease. Identifying transcriptional programs that maintain these neurons in the adult brain will help us understand their specific vulnerability. Here, we show that the survival of dopaminergic neurons requires the ongoing action of LIM-homeodomain transcription factors Lmx1a and Lmx1b. We discovered an Lmx1a/b-dependent pathway maintaining mitochondrial functions in midbrain dopaminergic neurons. Accordingly, ablation of Lmx1a/b results in impaired respiratory chain activity, increased oxidative stress, and mitochondrial DNA damage and causes Lewy neurite-like pathology. Importantly, deletion of Lmx1a/b links metabolic impairment, α-synuclein inclusions, and progressive neuronal loss. Modulation of this pathway opens new strategies to slow down or prevent the death of vulnerable neurons in Parkinson’s disease. (See pp. E4387–E4396.)
Endogenous N-acyl taurines regulate skin wound healing
Oscar Sasso, Silvia Pontis, Andrea Armirotti, Giorgia Cardinali, Daniela Kovacs, Marco Migliore, Maria Summa, Guillermo Moreno-Sanz, Mauro Picardo, and Daniele Piomelli
Healthy human skin quickly repairs itself when wounded. Skin healing is essential for survival, and it depends on a well-ordered sequence of molecular and cellular events that require the cooperation of several growth-promoting proteins released by skin cells or produced in the extracellular matrix. In the present study, we identify a family of lipid-derived molecules that accelerate the closure of self-repairing skin wounds. These endogenous substances promote migration of epidermal keratinocytes and differentiation of dermal fibroblasts by recruiting intracellular signals similar to those engaged by protein growth factors. Understanding this unprecedented mechanism of wound-healing control may guide new therapeutic approaches to the management of chronic wounds in patients with diabetes, bed-ridden elderly people with pressure ulcers, and immunosuppressed recipients of organ transplants. (See pp. E4397–E4406.)
A conserved amino acid residue critical for product and substrate specificity in plant triterpene synthases
Melissa Salmon, Ramesha B. Thimmappa, Robert E. Minto, Rachel E. Melton, Richard K. Hughes, Paul E. O’Maille, Andrew M. Hemmings, and Anne Osbourn
The triterpenes are a large and highly diverse group of plant natural products. They are synthesized by cyclization of the linear isoprenoid 2,3-oxidosqualene into different triterpene scaffolds by enzymes known as triterpene synthases. This cyclization process is one of the most complex enzymatic reactions known and is only poorly understood. Here, we identify a conserved amino acid residue that is critical for both product and substrate specificity in triterpene synthases from diverse plant species. Our results shed new light on mechanisms of triterpene cyclization in plants and open up the possibility of manipulating both the nature of the precursor and product specificity, findings that can be exploited for the production of diverse and novel triterpenes. (See pp. E4407–E4414.)
COP1 is required for UV-B–induced nuclear accumulation of the UVR8 photoreceptor
Ruohe Yin, Mariya Y. Skvortsova, Sylvain Loubéry, and Roman Ulm
Plant tissues are resistant to the potentially damaging UV-B radiation intrinsic to sunlight. UV-B photoreception by a UV RESISTANCE LOCUS 8 (UVR8) photoreceptor regulates gene expression in plants associated with UV-B acclimation and stress tolerance and with morphological changes. Mechanistically, UV-B photon reception by specific tryptophan residues of UVR8 homodimers results in monomerization and enhanced nuclear accumulation of UVR8. Active UVR8 monomers interact with the key signaling protein CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1). This UV-B–dependent interaction is a crucial step in signal propagation, but the link between this mechanism and UVR8 nuclear accumulation and gene expression remains ill defined. Our results emphasize the importance of nuclear-localized UVR8 and highlight a previously unknown activity of COP1 in mediating UVR8 nuclear accumulation in response to UV-B. (See pp. E4415–E4422.)
Allosteric proteins as logarithmic sensors
Noah Olsman and Lea Goentoro
Biological sensory systems have the capacity to respond to signals over a broad range of intensities, be it vision in animals or signal transduction in cells. Such a broad response range is thought to be mediated by the system’s ability to sense signal logarithmically. We seek to understand the implementation of logarithmic sensors in cells. We find that a pervasive class of proteins, those that are allosterically regulated, have dynamics that facilitate response on a logarithmic (as opposed to absolute) scale, allowing sensitive response across a broad range of signal. (See pp. E4423–E4430.)