Recent Submissions

  • Understanding High-Salt and Cold Adaptation of a Polyextremophilic Enzyme

    Karan, Ram; Mathew, Sam; Muhammad, Reyhan; Bautista, Didier B.; Vogler, Malvina M.; Eppinger, Jörg; Oliva, Romina; Cavallo, Luigi; Arold, Stefan T.; Rueping, Magnus (Microorganisms, MDPI AG, 2020-10-16) [Article]
    The haloarchaeon Halorubrum lacusprofundi is among the few polyextremophilic organisms capable of surviving in one of the most extreme aquatic environments on Earth, the Deep Lake of Antarctica (−18 °C to +11.5 °C and 21–28%, w/v salt content). Hence, H. lacusprofundi has been proposed as a model for biotechnology and astrobiology to investigate potential life beyond Earth. To understand the mechanisms that allow proteins to adapt to both salinity and cold, we structurally (including X-ray crystallography and molecular dynamics simulations) and functionally characterized the β-galactosidase from H. lacusprofundi (hla_bga). Recombinant hla_bga (produced in Haloferax volcanii) revealed exceptional stability, tolerating up to 4 M NaCl and up to 20% (v/v) of organic solvents. Despite being cold-adapted, hla_bga was also stable up to 60 °C. Structural analysis showed that hla_bga combined increased surface acidity (associated with halophily) with increased structural flexibility, fine-tuned on a residue level, for sustaining activity at low temperatures. The resulting blend enhanced structural flexibility at low temperatures but also limited protein movements at higher temperatures relative to mesophilic homologs. Collectively, these observations help in understanding the molecular basis of a dual psychrophilic and halophilic adaptation and suggest that such enzymes may be intrinsically stable and functional over an exceptionally large temperature range.
  • Interleukin-26 activates macrophages and facilitates killing of Mycobacterium tuberculosis

    Hawerkamp, Heike C.; van Geelen, Lasse; Korte, Jan; Di Domizio, Jeremy; Swidergall, Marc; Momin, Afaque Ahmad Imtiyaz; Guzmán-Vega, Francisco J.; Arold, Stefan T.; Ernst, Joachim; Gilliet, Michel; Kalscheuer, Rainer; Homey, Bernhard; Meller, Stephan (Scientific Reports, Springer Science and Business Media LLC, 2020-10-14) [Article]
    Abstract Tuberculosis-causing Mycobacterium tuberculosis (Mtb) is transmitted via airborne droplets followed by a primary infection of macrophages and dendritic cells. During the activation of host defence mechanisms also neutrophils and T helper 1 (TH1) and TH17 cells are recruited to the site of infection. The TH17 cell-derived interleukin (IL)-17 in turn induces the cathelicidin LL37 which shows direct antimycobacterial effects. Here, we investigated the role of IL-26, a TH1- and TH17-associated cytokine that exhibits antimicrobial activity. We found that both IL-26 mRNA and protein are strongly increased in tuberculous lymph nodes. Furthermore, IL-26 is able to directly kill Mtb and decrease the infection rate in macrophages. Binding of IL-26 to lipoarabinomannan might be one important mechanism in extracellular killing of Mtb. Macrophages and dendritic cells respond to IL-26 with secretion of tumor necrosis factor (TNF)-α and chemokines such as CCL20, CXCL2 and CXCL8. In dendritic cells but not in macrophages cytokine induction by IL-26 is partly mediated via Toll like receptor (TLR) 2. Taken together, IL-26 strengthens the defense against Mtb in two ways: firstly, directly due to its antimycobacterial properties and secondly indirectly by activating innate immune mechanisms.
  • A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions.

    Barylyuk, Konstantin; Koreny, Ludek; Ke, Huiling; Butterworth, Simon; Crook, Oliver M; Lassadi, Imen; Gupta, Vipul; Tromer, Eelco; Mourier, Tobias; Stevens, Tim J; Breckels, Lisa M; Pain, Arnab; Lilley, Kathryn S; Waller, Ross F (Cell host & microbe, Elsevier BV, 2020-10-14) [Article]
    Apicomplexan parasites cause major human disease and food insecurity. They owe their considerable success to highly specialized cell compartments and structures. These adaptations drive their recognition, nondestructive penetration, and elaborate reengineering of the host's cells to promote their growth, dissemination, and the countering of host defenses. The evolution of unique apicomplexan cellular compartments is concomitant with vast proteomic novelty. Consequently, half of apicomplexan proteins are unique and uncharacterized. Here, we determine the steady-state subcellular location of thousands of proteins simultaneously within the globally prevalent apicomplexan parasite Toxoplasma gondii. This provides unprecedented comprehensive molecular definition of these unicellular eukaryotes and their specialized compartments, and these data reveal the spatial organizations of protein expression and function, adaptation to hosts, and the underlying evolutionary trajectories of these pathogens.
  • MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells

    Sumida, Noriyuki; Sifakis, Emmanouil G; Kiani, Narsis A; Ronnegren, Anna Lewandowska; Scholz, Barbara A; Vestlund, Johanna; Gomez-Cabrero, David; Tegner, Jesper; Göndör, Anita; Ohlsson, Rolf (Nucleic Acids Research, Oxford University Press (OUP), 2020-10-11) [Article]
    Abstract The relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood. Using an innovated, ultra-sensitive technique, we address here enigmatic features underlying the communications between MYC and its enhancers in relation to the transcriptional process. MYC thus interacts with its flanking enhancers in a mutually exclusive manner documenting that enhancer hubs impinging on MYC detected in large cell populations likely do not exist in single cells. Dynamic encounters with pathologically activated enhancers responsive to a range of environmental cues, involved <10% of active MYC alleles at any given time in colon cancer cells. Being the most central node of the chromatin network, MYC itself likely drives its communications with flanking enhancers, rather than vice versa. We submit that these features underlie an acquired ability of MYC to become dynamically activated in response to a diverse range of environmental cues encountered by the cell during the neoplastic process.
  • SARS-CoV-2 S1 and N-based serological assays reveal rapid seroconversion and induction of specific antibody response in COVID-19 patients

    Algaissi, Abdullah; Alfaleh, Mohamed A.; Hala, Sharif; Abujamel, Turki S.; Alamri, Sawsan S.; Almahboub, Sarah A.; Alluhaybi, Khalid A.; Hobani, Haya I.; Alsulaiman, Reem M.; AlHarbi, Rahaf H.; ElAssouli, M.-Z.aki; Alhabbab, Rowa Y.; AlSaieedi, Ahdab A.; Abdulaal, Wesam H.; AL-Somali, Afrah A.; Alofi, Fadwa S.; Khogeer, Asim A.; Alkayyal, Almohanad A.; Mahmoud, Ahmad Bakur; Almontashiri, Naif A. M.; Pain, Arnab; Hashem, Anwar M. (Scientific Reports, Springer Science and Business Media LLC, 2020-10-06) [Article]
    Abstract As the Coronavirus Disease 2019 (COVID-19), which is caused by the novel SARS-CoV-2, continues to spread rapidly around the world, there is a need for well validated serological assays that allow the detection of viral specific antibody responses in COVID-19 patients or recovered individuals. In this study, we established and used multiple indirect Enzyme Linked Immunosorbent Assay (ELISA)-based serological assays to study the antibody response in COVID-19 patients. In order to validate the assays we determined the cut off values, sensitivity and specificity of the assays using sera collected from pre-pandemic healthy controls, COVID-19 patients at different time points after disease-onset, and seropositive sera to other human coronaviruses (CoVs). The developed SARS-CoV-2 S1 subunit of the spike glycoprotein and nucleocapsid (N)-based ELISAs not only showed high specificity and sensitivity but also did not show any cross-reactivity with other CoVs. We also show that all RT-PCR confirmed COVID-19 patients tested in our study developed both virus specific IgM and IgG antibodies as early as week one after disease onset. Our data also suggest that the inclusion of both S1 and N in serological testing would capture as many potential SARS-CoV-2 positive cases as possible than using any of them alone. This is specifically important for tracing contacts and cases and conducting large-scale epidemiological studies to understand the true extent of virus spread in populations.
  • Single crystal, Hirshfeld surface and theoretical analysis of methyl 4-hydroxybenzoate, a common cosmetic, drug and food preservative—Experiment versus theory

    Sharfalddin, Abeer; Davaasuren, Bambar; Emwas, Abdul-Hamid M.; Jaremko, Mariusz; Jaremko, Lukasz; Hussien, Mostafa (PLOS ONE, Public Library of Science (PLoS), 2020-10-06) [Article]
    Methyl 4-hydroxybenzoate, commonly known as methyl paraben, is an anti-microbial agent used in cosmetics and personal-care products, and as a food preservative. In this study, the single crystal X-ray structure of methyl 4-hydroxybenzoate was determined at 120 K. The crystal structure comprises three methyl 4-hydroxybenzoate molecules condensed to a 3D framework via extensive intermolecular hydrogen bonding. Hirshfeld surface analysis was performed to determine the intermolecular interactions and the crystal packing. In addition, computational calculations of methyl 4-hydroxybenzoate were obtained using the Gaussian 09W program, and by quantum mechanical methods, Hartree Fock (HF) and Density Functional Theory (DFT) with the 6–311G(d,p) basis set. The experimental FT-IR spectrum strongly correlated with the computed vibrational spectra (R2 = 0.995). The energies of the frontier orbitals, HOMO and LUMO, were used to calculate the chemical quantum parameters. The lower band gap value (ΔE) indicates the molecular determinants underlying the known pharmaceutical activity of the molecule.
  • The Best Peptidomimetic Strategies to Undercover Antibacterial Peptides

    Lachowicz, Joanna Izabela; Szczepski, Kacper; Scano, Alessandra; Casu, Cinzia; Fais, Sara; Orrù, Germano; Pisano, Barbara; Piras, Monica; Jaremko, Mariusz (International Journal of Molecular Sciences, MDPI AG, 2020-10-05) [Article]
    Health-care systems that develop rapidly and efficiently may increase the lifespan of humans. Nevertheless, the older population is more fragile, and is at an increased risk of disease development. A concurrently growing number of surgeries and transplantations have caused antibiotics to be used much more frequently, and for much longer periods of time, which in turn increases microbial resistance. In 1945, Fleming warned against the abuse of antibiotics in his Nobel lecture: “The time may come when penicillin can be bought by anyone in the shops. Then there is the danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug make them resistant”. After 70 years, we are witnessing the fulfilment of Fleming’s prophecy, as more than 700,000 people die each year due to drug-resistant diseases. Naturally occurring antimicrobial peptides protect all living matter against bacteria, and now different peptidomimetic strategies to engineer innovative antibiotics are being developed to defend humans against bacterial infections.
  • Genetic mapping of the early responses to salt stress in Arabidopsis thaliana

    Awlia, Mariam; Alshareef, Nouf Owdah Hameed; Saber, Noha; Korte, Arthur; Oakey, Helena; Panzarova, Klara; Trtilek, Martin; Negrão, Sónia; Tester, Mark A.; Julkowska, Magdalena M. (Cold Spring Harbor Laboratory, 2020-10-04) [Preprint]
    Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single setup is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from one hour to seven days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (Fv'/Fm') greatly affected growth maintenance in the early phase of salt stress, while maximum quantum yield (QY max) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QY max and Fv'/Fm' were selected for validation using T-DNA insertion lines. We characterised an unknown protein kinase found in the QY max locus, which reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the identified candidate genes will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses, while identifying associations across different traits and time points, which likely constitute the genetic components of salinity tolerance.
  • Regulation of kinase activity by combined action of juxtamembrane and C-terminal regions of receptors

    Lin, Chi-Chuan; Wieteska, Lukasz; Poncet-Montange, Guillaume; Suen, Kin Man; Arold, Stefan T.; ahmed, zamal; Ladbury, John Edward (Cold Spring Harbor Laboratory, 2020-10-01) [Preprint]
    Despite the kinetically-favorable, ATP-rich intracellular environment, the mechanism by which receptor tyrosine kinases (RTKs) repress activation prior to extracellular stimulation is poorly understood. RTKs are activated through a precise sequence of phosphorylation reactions starting with a tyrosine on the activation loop (A-loop) of the intracellular kinase domain (KD). This forms an essential mono-phosphorylated active intermediate state on the path to further phosphorylation of the receptor. We show that this state is subjected to stringent control imposed by the peripheral juxtamembrane (JM) and C-terminal tail (CT) regions. This entails interplay between the intermolecular interaction between JM with KD, which stabilizes the asymmetric active KD dimer, and the opposing intramolecular binding of CT to KD. A further control step is provided by the previously unobserved direct binding between JM and CT. Mutations in JM and CT sites that perturb regulation are found in numerous pathologies, revealing novel sites for potential pharmaceutical intervention.
  • Suaeda vermiculata Aqueous-Ethanolic Extract-Based Mitigation of CCl4-Induced Hepatotoxicity in Rats, and HepG-2 and HepG-2/ADR Cell-Lines-Based Cytotoxicity Evaluations

    Mohammed, Salman A. A.; Khan, Riaz A.; El-Readi, Mahmoud Z.; Emwas, Abdul-Hamid M.; Sioud, Salim; Poulson, Benjamin Gabriel; Jaremko, Mariusz; Eldeeb, Hussein M.; Al-Omar, Mohsen S.; Mohammed, Hamdoon A. (Plants, MDPI AG, 2020-09-30) [Article]
    Suaeda vermiculata, an edible halophytic plant, used by desert nomads to treat jaundice, was investigated for its hepatoprotective bioactivity and safety profile on its mother liquor aqueous-ethanolic extract. Upon LC-MS (Liquid Chromatography-Mass Spectrometry) analysis, the presence of several constituents including three major flavonoids, namely quercetin, quercetin-3-O-rutinoside, and kaempferol-O-(acetyl)-hexoside-pentoside were confirmed. The aqueous-ethanolic extract, rich in antioxidants, quenched the DPPH (1,1-diphenyl-2-picrylhydrazyl) radicals, and also showed noticeable levels of radical scavenging capacity in ABTS (2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid) assay. For the hepatoprotective activity confirmation, the male rat groups were fed daily, for 7 days (n = 8/group, p.o.), either carboxyl methylcellulose (CMC) 0.5%, silymarin 200 mg/kg, the aqueous-ethanolic extract of the plant Suaeda vermiculata (100, 250, and 500 mg/kg extract), or quercetin (100 mg/kg) alone, and on day 7 of the administrations, all the animal groups, excluding a naïve (250 mg/kg aqueous-ethanolic extract-fed), and an intact animal group were induced hepatotoxicity by intraperitoneally administering carbon tetrachloride (CCl4). All the animals were sacrificed after 24 h, and aspartate transaminase and alanine transaminase serum levels were observed, which were noted to be significantly decreased for the aqueous-ethanolic extract, silymarin, and quercetin-fed groups in comparison to the CMC-fed group (p < 0.0001). No noticeable adverse effects were observed on the liver, kidney, or heart’s functions of the naïve (250 mg/kg) group. The aqueous-ethanolic extract was found to be safe in the acute toxicity (5 g/kg) test and showed hepatoprotection and safety at higher doses. Further upon, the cytotoxicity testings in HepG-2 and HepG-2/ADR (Adriamycin resistant) cell-lines were also investigated, and the IC50 values were recorded at 56.19±2.55 µg/mL, and 78.40±0.32 µg/mL (p < 0.001, Relative Resistance RR 1.39), respectively, while the doxorubicin (Adriamycin) IC50 values were found to be 1.3±0.064, and 4.77±1.05 µg/mL (p < 0.001, RR 3.67), respectively. The HepG-2/ADR cell-lines when tested in a combination of the aqueous-ethanolic extract with doxorubicin, a significant reversal in the doxorubicin’s IC50 value by 2.77 folds (p < 0.001, CI = 0.56) was noted as compared to the cytotoxicity test where the extract was absent. The mode of action for the reversal was determined to be synergistic in nature indicating the role of the aqueous-ethanolic extract.
  • Establishment of iPSC lines from a high-grade Klinefelter Syndrome patient (49-XXXXY) and two genetically matched healthy relatives (KAUSTi003-A, KAUSTi004-A, KAUSTi004-B, KAUSTi005-A, KAUSTi005-B, KAUSTi005-C).

    Alowaysi, Maryam; Fiacco, Elisabetta; Astro, Veronica; Adamo, Antonio (Stem cell research, Elsevier BV, 2020-09-28) [Article]
    Klinefelter Syndrome (KS) is the most frequent X chromosome aneuploidy in males. KS patients with 47-XXY, 48-XXXY and 49-XXXXY karyotypes endure inter-individual phenotypic variabilities including infertility, cardiac diseases, metabolic and psychiatric disorders. We derived iPSC lines from a high-grade 49-XXXXY KS and two healthy donors' fibroblasts. Importantly, the healthy controls XY and XX are direct relatives to KS patients, thus enabling functional comparisons of healthy and disease iPSCs with partially matched genetic backgrounds. These iPSC lines provide an unprecedented cellular tool to study KS pathophysiology at the pluripotent stage as well as during differentiation into disease relevant cell types.
  • Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes

    Zaric, Bozidarka L.; Radovanovic, Jelena N.; Gluvic, Zoran; Stewart, Alan J.; Essack, Magbubah; Motwalli, Olaa; Gojobori, Takashi; Isenovic, Esma R. (Frontiers in Immunology, Frontiers Media SA, 2020-09-28) [Article]
    Cardiovascular disease is the leading global health concern and responsible for more deaths worldwide than any other type of disorder. Atherosclerosis is a chronic inflammatory disease in the arterial wall, which underpins several types of cardiovascular disease. It has emerged that a strong relationship exists between alterations in amino acid (AA) metabolism and the development of atherosclerosis. Recent studies have reported positive correlations between levels of branched-chain amino acids (BCAAs) such as leucine, valine, and isoleucine in plasma and the occurrence of metabolic disturbances. Elevated serum levels of BCAAs indicate a high cardiometabolic risk. Thus, BCAAs may also impact atherosclerosis prevention and offer a novel therapeutic strategy for specific individuals at risk of coronary events. The metabolism of AAs, such as L-arginine, homoarginine, and L-tryptophan, is recognized as a critical regulator of vascular homeostasis. Dietary intake of homoarginine, taurine, and glycine can improve atherosclerosis by endothelium remodeling. Available data also suggest that the regulation of AA metabolism by indoleamine 2,3-dioxygenase (IDO) and arginases 1 and 2 are mediated through various immunological signals and that immunosuppressive AA metabolizing enzymes are promising therapeutic targets against atherosclerosis. Further clinical studies and basic studies that make use of animal models are required. Here we review recent data examining links between AA metabolism and the development of atherosclerosis.
  • Le symptôme entre neurosciences et psychanalyse. Actualité de l’au-delà du principe de plaisir

    Ansermet, François; Magistretti, Pierre J. (Figures de la psychanalyse, CAIRN, 2020-09-24) [Article]
    Asking the question of current affairs implies that of knowing if we can really access what is current, what is present. Saying the present excludes its existence. Nietzsche said of the present that it is inactual. Such is its fundamental contradiction, the contradiction peculiar to the contemporary. Perhaps it is only possible to tell the topicality of something from its aftermath. This is the case with the symptom which, paradoxically, finds its place as a symptom through the after-effects of the analytical treatment, whereas, in the moment of life, it only asserts itself. The symptom is a complex articulation of the relation to time. It brings together, in itself, the present of the past, the present of the present and the present of the future. In any case, the symptom declines in time in a paradoxical way. The symptom is a present that persists, an inactual present that insists, bringing into play the topicality of an inactivity that goes beyond the subject. Another dimension of the symptom is the coincidence it implies between the most intimate and the most political. And one could say that every symptom is both intimate and political, because fundamentally, the symptom brings together both an origin and an incidence which happen to be simultaneously intimate and political - another way of repeating the statement of Freud on the link between the individual and the social, when he posits individual psychology as being also, “from the outset and simultaneously, a social psychology, in this broadened but perfectly justified sense ...
  • Thermally stable surfactant-free ceria nanocubes in silica aerogel

    Caddeo, Francesco; Casu, Alberto; Loche, Danilo; Morgan, Lucy M.; Mountjoy, Gavin; O'Regan, Colm; Casula, Maria F.; Hayama, Shusaku; Corrias, Anna; Falqui, Andrea (Journal of Colloid and Interface Science, Elsevier BV, 2020-09-22) [Article]
    Surfactant-mediated chemical routes allow one to synthesize highly engineered shape- and size-controlled nanocrystals. However, the occurrence of capping agents on the surface of the nanocrystals is undesirable for selected applications. Here, a novel approach to the production of shape-controlled nanocrystals which exhibit high thermal stability is demonstrated. Ceria nanocubes obtained by surfactant-mediated synthesis are embedded inside a highly porous silica aerogel and thermally treated to remove the capping agent. Powder X-ray Diffraction and Scanning Transmission Electron Microscopy show the homogeneous dispersion of the nanocubes within the aerogel matrix. Remarkably, both the size and the shape of the ceria nanocubes are retained not only throughout the aerogel syntheses but also upon thermal treatments up to 900 °C, while avoiding their agglomeration. The reactivity of ceria is measured by in situ High-Energy Resolution Fluorescence Detected - X-ray Absorption Near Edge Spectroscopy at the Ce L3 edge, and shows the reversibility of redox cycles of ceria nanocubes when they are embedded in the aerogel. This demonstrates that the enhanced reactivity due to their prominent {1 0 0} crystal facets is preserved. In contrast, unsupported ceria nanocubes begin to agglomerate as soon as the capping agent decomposes, leading to a degradation of their reactivity already at 275 °C.
  • Striatal infusion of cholesterol promotes dose-dependent behavioral benefits and exerts disease-modifying effects in Huntington's disease mice

    Birolini, Giulia; Valenza, Marta; Di Paolo, Eleonora; Vezzoli, Elena; Talpo, Francesca; Maniezzi, Claudia; Caccia, Claudio; Leoni, Valerio; Taroni, Franco; Bocchi, Vittoria D; Conforti, Paola; Sogne, Elisa; Petricca, Lara; Cariulo, Cristina; Verani, Margherita; Caricasole, Andrea; Falqui, Andrea; Biella, Gerardo; Cattaneo, Elena (EMBO Molecular Medicine, EMBO, 2020-09-22) [Article]
    A variety of pathophysiological mechanisms are implicated in Huntington's disease (HD). Among them, reduced cholesterol biosynthesis has been detected in the HD mouse brain from pre-symptomatic stages, leading to diminished cholesterol synthesis, particularly in the striatum. In addition, systemic injection of cholesterol-loaded brain-permeable nanoparticles ameliorates synaptic and cognitive function in a transgenic mouse model of HD. To identify an appropriate treatment regimen and gain mechanistic insights into the beneficial activity of exogenous cholesterol in the HD brain, we employed osmotic mini-pumps to infuse three escalating doses of cholesterol directly into the striatum of HD mice in a continuous and rate-controlled manner. All tested doses prevented cognitive decline, while amelioration of disease-related motor defects was dose-dependent. In parallel, we found morphological and functional recovery of synaptic transmission involving both excitatory and inhibitory synapses of striatal medium spiny neurons. The treatment also enhanced endogenous cholesterol biosynthesis and clearance of mutant Huntingtin aggregates. These results indicate that cholesterol infusion to the striatum can exert a dose-dependent, disease-modifying effect and may be therapeutically relevant in HD.
  • Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair

    Tsutakawa, Susan E.; Tsai, Chi-Lin; Yan, Chunli; Bralic, Amer; Chazin, Walter J.; Hamdan, Samir; Schärer, Orlando D.; Ivanov, Ivaylo; Tainer, John A. (DNA Repair, Elsevier BV, 2020-09-17) [Article]
    Critical for transcription initiation and bulky lesion DNA repair, TFIIH provides an exemplary system to connect molecular mechanisms to biological outcomes due to its strong genetic links to different specific human diseases. Recent advances in structural and computational biology provide a unique opportunity to re-examine biologically relevant molecular structures and develop possible mechanistic insights for the large dynamic TFIIH complex. TFIIH presents many puzzles involving how its two SF2 helicase family enzymes, XPB and XPD, function in transcription initiation and repair: how do they initiate transcription, detect and verify DNA damage, select the damaged strand for incision, coordinate repair with transcription and cell cycle through Cdkactivating-kinase (CAK) signaling, and result in very different specific human diseases associated with cancer, aging, and development from single missense mutations? By joining analyses of breakthrough cryo-electron microscopy (cryo-EM) structures and advanced computation with data from biochemistry and human genetics, we develop unified concepts and molecular level understanding for TFIIH functions with a focus on structural mechanisms. We provocatively consider that TFIIH may have first evolved from evolutionary pressure for TCR to resolve arrested transcription blocks to DNA replication and later added its key roles in transcription initiation and global DNA repair. We anticipate that this level of mechanistic information will have significant impact on thinking about TFIIH, laying a robust foundation suitable to develop new paradigms for DNA transcription initiation and repair along with insights into disease prevention, susceptibility, diagnosis and interventions.
  • Stimulated Raman microspectroscopy as a new method to classify microfibers from environmental samples

    Laptenok, Siarhei; Martin, Cecilia; Genchi, Luca; Duarte, Carlos M.; Liberale, Carlo (Environmental Pollution, Elsevier BV, 2020-09-16) [Article]
    Capsule: We present Stimulated Raman Microscopy as a new method to reliably classify environmental microfibers. The majority of analyzed microfibers were of natural origin.
  • Arginine citrullination of proteins as a specific response mechanism in Arabidopsis thaliana

    Marondedze, Claudius; Elia, Giuliano; Thomas, Ludivine; Wong, Aloysius; Gehring, Christoph A (Cold Spring Harbor Laboratory, 2020-09-13) [Preprint]
    Arginine citrullination, also referred to as arginine deimination, is a post-translational modification involved in an increasing number of physiological processes in animals, including histone modifications and transcriptional regulation, and in severe diseases such as rheumatoid arthritis and neurodegenerative conditions. It occurs when arginine side chains are deiminated and converted into side chains of the amino acid citrulline, a process catalysed by a family of Ca2+-dependent peptidyl arginine deiminases (PADs). PADs have been discovered in several mammalian species and in other vertebrates, like birds and fish, but have not been observed in bacteria, lower eukaryotes or higher plants. Here we show, firstly, that the Arabidopsis thaliana proteome does contain citrullinated proteins; secondly and importantly, that the citrullination signature changes in response to cold stress. Among the citrullinated proteins are DNA- or RNA-binding proteins thus implying a role for it the control of the transcriptional programming in plant cells. Thirdly, through sequence and structural analysis, we identify one arabidopsis protein, currently annotated as agmatine deiminase (At5g08170), as a candidate protein arginine deiminase. Finally, we show biochemical evidence that AT5G08170 can citrullinate peptides from LHP1-interacting factor 2 (AT4G00830) an RNA-binding protein that has been identified as citrullinated in cell suspension cultures of Arabidopsis thaliana roots. In addition, we show that, in vitro, agmatine deiminase can undergo auto-citrullination. In conclusion, our work established the presence of protein arginine citrullination in higher plants and assigns it a role in post-translational modifications during abiotic stress responses.
  • Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics

    Kharchenko, Vladlena; Nowakowski, Michal; Jaremko, Mariusz; Ejchart, Andrzej; Jaremko, Lukasz (Journal of Biomolecular NMR, Springer Science and Business Media LLC, 2020-09-12) [Article]
    Abstract Intramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature.
  • Characterizing a strong pan-muscular promoter (Pmlc-1) as a fluorescent co-injection marker to select for single-copy insertions.

    El Mouridi, Sonia; Peng, Yuli; Frøkjær-Jensen, Christian (microPublication biology, 2020-09-10) [Article]
    Fluorescent markers are useful for identifying transgenic C. elegans after injection. In some cases, fluorophores are used to identify transgenics and to propagate animals with extra-chromosomal or integrated arrays (e.g., sur-5

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