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Tom E J Theunissen, Radek Szklarczyk, Mike Gerards, Debby M E I Hellebrekers, Elvira N M Mulder-Den Hartog, Jo Vanoevelen, Rick Kamps, Bart de Koning, S Lane Rutledge, Thomas Schmitt-Mechelke, Carola G M van Berkel, Marjo S van der Knaap, Irenaeus F M de Coo, Hubert J M Smeets
In establishing a genetic diagnosis in heterogeneous neurological disease, clinical characterization and whole exome sequencing (WES) go hand-in-hand. Clinical data are essential, not only to guide WES variant selection and define the clinical severity of a genetic defect but also to identify other patients with defects in the same gene. In an infant patient with sensorineural hearing loss, psychomotor retardation, and epilepsy, WES resulted in identification of a novel homozygous CLPP frameshift mutation (c...
2016: Frontiers in Neurology
Elizabeth Culp, Gerard D Wright
Bacterial proteases are an extensive collection of enzymes that have vital roles in cell viability, stress response and pathogenicity. Although their perturbation clearly offers the potential for antimicrobial drug development, both as traditional antibiotics and anti-virulence drugs, they are not yet the target of any clinically used therapeutics. Here we describe the potential for and recent progress in the development of compounds targeting bacterial proteases with a focus on AAA+ family proteolytic complexes and signal peptidases (SPs)...
November 30, 2016: Journal of Antibiotics
Kyle A Pelot, Rod Mitchell, Moonhyuk Kwon, David M Hagelthorn, Jacob F Wardman, Angela Chiang, Jörg Bohlmann, Dae-Kyun Ro, Philipp Zerbe
Salvia divinorum commonly known as diviner's sage, is an ethnomedicinal plant of the mint family (Lamiaceae). S. divinorum is rich in clerodane-type diterpenoids, which accumulate predominantly in leaf glandular trichomes. The main bioactive metabolite, salvinorin A, is the first non-nitrogenous natural compound known to function as an opioid-receptor agonist, and is undergoing clinical trials for potential use in treating neuropsychiatric diseases and drug addictions. We report here the discovery and functional characterization of two S...
November 19, 2016: Plant Journal: for Cell and Molecular Biology
Fei Ye, Jiahui Li, Cai-Guang Yang
The global spread of antibiotic resistance among important human pathogens emphasizes the need to find new antibacterial drugs with a novel mode of action. The ClpP protease has been shown to demonstrate its pivotal importance to both the survival and the virulence of pathogenic bacteria during host infection. Deregulating ClpP activity either through overactivation or inhibition could lead to antibacterial activity, declaiming the dual molecular mechanism for small-molecule modulation. Recently, natural products acyldepsipeptides (ADEPs) have been identified as a new class of antibiotics that activate ClpP to a dysfunctional state in the absence of cognate ATPases...
November 10, 2016: Molecular BioSystems
Laura Díaz-Sáez, Genady Pankov, William N Hunter
Caseinolytic proteases are large oligomeric assemblies responsible for maintaining protein homeostasis in bacteria and in so doing influence a wide range of biological processes. The functional assembly involves three chaperones together with the oligomeric caseinolytic protease catalytic subunit P (ClpP). This protease represents a potential target for therapeutic intervention in pathogenic bacteria. Here, we detail an efficient protocol for production of recombinant ClpP from Francisella tularensis, and the structural characterization of three crystal forms which grow under similar conditions...
November 1, 2016: Proteins
Karolina Szczepanowska, Priyanka Maiti, Alexandra Kukat, Eduard Hofsetz, Hendrik Nolte, Katharina Senft, Christina Becker, Benedetta Ruzzenente, Hue-Tran Hornig-Do, Rolf Wibom, Rudolf J Wiesner, Marcus Krüger, Aleksandra Trifunovic
Despite being one of the most studied proteases in bacteria, very little is known about the role of ClpXP in mitochondria. We now present evidence that mammalian CLPP has an essential role in determining the rate of mitochondrial protein synthesis by regulating the level of mitoribosome assembly. Through a proteomic approach and the use of a catalytically inactive CLPP, we produced the first comprehensive list of possible mammalian ClpXP substrates involved in the regulation of mitochondrial translation, oxidative phosphorylation, and a number of metabolic pathways...
December 1, 2016: EMBO Journal
Qiwen Hu, Huagang Peng, Xiancai Rao
Vancomycin has been used as the last resort in the clinical treatment of serious Staphylococcus aureus infections. Vancomycin-intermediate S. aureus (VISA) was discovered almost two decades ago. Aside from the vancomycin-intermediate phenotype, VISA strains from the clinic or laboratory exhibited common characteristics, such as thickened cell walls, reduced autolysis, and attenuated virulence. However, the genetic mechanisms responsible for the reduced vancomycin susceptibility in VISA are varied. The comparative genomics of vancomycin-susceptible S...
2016: Frontiers in Microbiology
W Y Zhang, X P Zhang, J W Chen, Y R Sun, J Wang, H Hu, K X Xu
OBJECTIVE: To investigate age related changes in urodynamic parameters of women with urinary incontinence. METHODS: From May 2008 to October 2015, a total of 214 patients diagnosed with urinary incontinence in Peking University People's Hospital was involved in this study. Average age was (56.97±10.68) years, ranging from 30 to 82 years, and average history was (8.44±8.85) years, ranging from one month to 50 years. Urodynamic examinations of each patient were taken before operation routinely in Department of Urology, Peking University People's Hospital...
October 18, 2016: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
Débora Broch Trentini, Marcin Józef Suskiewicz, Alexander Heuck, Robert Kurzbauer, Luiza Deszcz, Karl Mechtler, Tim Clausen
Protein turnover is a tightly controlled process critical for the removal of aberrant polypeptides and for cellular signalling. Whereas ubiquitin marks eukaryotic proteins for proteasomal degradation, a general tagging system for the equivalent bacterial Clp proteases is not known. Here we address the targeting mechanism of the ClpC:ClpP proteolytic complex from Bacillus subtilis. Quantitative affinity proteomics using a ClpP trapping mutant show that proteins phosphorylated on arginine residues are selectively targeted to ClpC:ClpP...
October 6, 2016: Nature
Neil J Sargentini, Nicholas P Gularte, Deborah A Hudman
A set of 3907 single-gene knockout (Keio collection) strains of Escherichia coli K-12 was examined for strains with increased susceptibility to killing by X- or UV-radiation. After screening with a high-throughput resazurin-based assay and determining radiation survival with triplicate clonogenic assays, we identified 76 strains (and associated deleted genes) showing statistically-significant increased radiation sensitivity compared to a control strain. To determine gene novelty, we constructed a reference database comprised of genes found in nine similar studies including ours...
November 2016: Mutation Research
A D Samarajeewa, J R Velicogna, J I Princz, R M Subasinghe, R P Scroggins, L A Beaudette
Silver nano-particles (AgNPs) are widely used in a range of consumer products as a result of their antimicrobial properties. Given the broad spectrum of uses, AgNPs have the potential for being released to the environment. As a result, environmental risks associated with AgNPs need to be assessed to aid in the development of regulatory guidelines. Research was performed to assess the effects of AgNPs on soil microbial activity and diversity in a sandy loam soil with an emphasis on using a battery of microbial tests involving multiple endpoints...
January 2017: Environmental Pollution
Peng-Cheng Fu, Yan-Zhao Zhang, Hui-Min Geng, Shi-Long Chen
BACKGROUND: The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). METHODS: Using high throughput sequencing technology, we got the complete nucleotide sequence of the G...
2016: PeerJ
T H Samigullin, M D Logacheva, E I Terenteva, G V Degtjareva, C M Vallejo-Roman
This work reports the complete plastid (pt) DNA sequence of Seseli montanum L. of the Apiaceae family, determined using next-generation sequencing technology. The complete genome sequence has been deposited in GenBank with accession No. KM035851. The S. montanum plastome is 147,823 bp in length. The plastid genome has a typical structure for angiosperms and contains a large single-copy region (LSC) of 92,620 bp and a small single-copy region (SSC) of 17,481 bp separated by a pair of 18,861 bp inverted repeats (IRa and IRb)...
September 2016: Biochemistry. Biokhimii︠a︡
Huan Wang, Zhongling Yang, Shuo Du, Lin Ma, Yao Liao, Yujie Wang, Ian Toth, Jiaqin Fan
Identifying phytopathogen proteins that are differentially expressed in the course of establishing an infection is important to better understand the infection process. In vitro approaches, using plant extracts added to culture medium, have been used to identify such proteins but the biological relevance of these findings for in planta infection are often uncertain until confirmed by in vivo studies. Here, we compared proteins of Pectobacterium carotovorum subsp. carotovorum strain PccS1 differentially expressed in LB medium supplemented with extracts of the ornamental plant Zantedeschia elliotiana cultivar 'Black magic' (in vitro) and in plant tissues (in vivo) by two-dimensional electrophoresis coupled with mass spectrometry...
September 27, 2016: Molecular Plant Pathology
Konstantia Georgouli, Jesus Martinez Del Rincon, Anastasios Koidis
The main objective of this work was to develop a novel dimensionality reduction technique as a part of an integrated pattern recognition solution capable of identifying adulterants such as hazelnut oil in extra virgin olive oil at low percentages based on spectroscopic chemical fingerprints. A novel Continuous Locality Preserving Projections (CLPP) technique is proposed which allows the modelling of the continuous nature of the produced in-house admixtures as data series instead of discrete points. The maintenance of the continuous structure of the data manifold enables the better visualisation of this examined classification problem and facilitates the more accurate utilisation of the manifold for detecting the adulterants...
February 15, 2017: Food Chemistry
Justine Lerat, Laurence Jonard, Natalie Loundon, Sophie Christin-Maitre, Didier Lacombe, Cyril Goizet, Cécile Rouzier, Lionel Van Maldergem, Souad Gherbi, Eréa-Nöel Garabedian, Jean-Paul Bonnefont, Philippe Touraine, Isabelle Mosnier, Arnold Munnich, Françoise Denoyelle, Sandrine Marlin
Perrault syndrome (PS) is a rare autosomal recessive condition characterized by deafness and gonadic dysgenesis. Recently, mutations in five genes have been identified: C10orf2, CLPP, HARS2, HSD17B4, and LARS2. Probands included are presented with sensorineural deafness associated with gonadic dysgenesis. DNA was sequenced using next-generation sequencing (NGS) with a panel of 35 deafness genes including the five Perrault genes. Exonic variations known as pathogenic mutations or detected with <1% frequency in public databases were extracted and subjected to segregation analysis within each family...
December 2016: Human Mutation
Lucas D Lopes, Michele de Cássia Pereira E Silva, Fernando D Andreote
The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane...
2016: Frontiers in Microbiology
Ane H Medeiros, Fabiana B Mingossi, Renata O Dias, Flávia P Franco, Renato Vicentini, Marcia O Mello, Daniel S Moura, Marcio C Silva-Filho
Sugarcane's (Saccharum spp.) response to Diatraea saccharalis (F.) (Lepidoptera: (Crambidae) herbivory was investigated using a macroarray spotted with 248 sugarcane Expressed Sequence Tags (ESTs) encoding serine peptidase inhibitors, serine peptidases. and Clp protease system subunits. Our results showed that after nine hours of herbivory, 13 sugarcane genes were upregulated and nine were downregulated. Among the upregulated genes, nine were similar to serine peptidase inhibitors and four were similar to Bowman-Birk Inhibitors (BBIs)...
2016: International Journal of Molecular Sciences
Wen-Cai Wang, Si-Yun Chen, Xian-Zhi Zhang
Actinidiaceae is a well-known economically important plant family in asterids. To elucidate the chloroplast (cp) genome evolution within this family, here we present complete genomes of three species from two sister genera (Clematoclethra and Actinidia) in the Actinidiaceae via genome skimming technique. Comparative analyses revealed that the genome structure and content were rather conservative in three cp genomes in spite of different inheritance pattern, i.e.paternal in Actinidia and maternal in Clematoclethra...
2016: PloS One
Yonggang Xu, Wantai Yu, Qiang Ma, Jing Wang, Hua Zhou, Chunming Jiang
Elevated concentrations of heavy metals and antibiotics often coexist in agricultural soils due to land application of large amounts of animal manure. The experiment was conducted to investigate the single and joint effects of different concentrations of sulfadiazine (SDZ) (10mgkg(-1) and 100mgkg(-1)) and copper (Cu) (20mgkg(-1) and 200mgkg(-1)) on soil microbial activity, i.e. fluorescein diacetate (FDA) hydrolysis, dehydrogenase (DHA) and basal respiration (BR), microbial biomass and community structure estimated using phospholipid fatty acids (PLFA), and community level physiological profiles (CLPP) using MicroResp™...
August 29, 2016: Ecotoxicology and Environmental Safety
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