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https://www.readbyqxmd.com/read/28536693/the-essential-role-of-clpxp-in-caulobacter-crescentus-requires-species-constrained-substrate-specificity
#1
Robert H Vass, Jacob Nascembeni, Peter Chien
The ClpXP protease is a highly conserved AAA+ degradation machine that is present throughout bacteria and in eukaryotic organelles. ClpXP is essential in some bacteria, such as Caulobacter crescentus, but dispensible in others, such as Escherichia coli. In Caulobacter, ClpXP normally degrades the SocB toxin and increased levels of SocB result in cell death. ClpX can be deleted in cells lacking this toxin, but these ΔclpX strains are still profoundly deficient in morphology and growth supporting the existence of additional important functions for ClpXP...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28523271/the-protein-chaperone-clpx-targets-native-and-non-native-aggregated-substrates-for-remodeling-disassembly-and-degradation-with-clpp
#2
Christopher J LaBreck, Shannon May, Marissa G Viola, Joseph Conti, Jodi L Camberg
ClpX is a member of the Clp/Hsp100 family of ATP-dependent chaperones and partners with ClpP, a compartmentalized protease, to degrade protein substrates bearing specific recognition signals. ClpX targets specific proteins for degradation directly or with substrate-specific adaptor proteins. Native substrates of ClpXP include proteins that form large oligomeric assemblies, such as MuA, FtsZ, and Dps in Escherichia coli. To remodel large oligomeric substrates, ClpX utilizes multivalent targeting strategies and discriminates between assembled and unassembled substrate conformations...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28522861/comparative-analysis-of-dendrobium-plastomes-and-utility-of-plastomic-mutational-hotspots
#3
Niu Zhitao, Zhu Shuying, Pan Jiajia, Li Ludan, Sun Jing, Ding Xiaoyu
Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515737/the-complete-plastome-sequences-of-four-orchid-species-insights-into-the-evolution-of-the-orchidaceae-and-the-utility-of-plastomic-mutational-hotspots
#4
Zhitao Niu, Qingyun Xue, Shuying Zhu, Jing Sun, Wei Liu, Xiaoyu Ding
Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28490437/high-throughput-crispri-phenotyping-identifies-new-essential-genes-in-streptococcus-pneumoniae
#5
Xue Liu, Clement Gallay, Morten Kjos, Arnau Domenech, Jelle Slager, Sebastiaan P van Kessel, Kèvin Knoops, Robin A Sorg, Jing-Ren Zhang, Jan-Willem Veening
Genome-wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn-seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%)...
May 10, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28455142/a-fish-oil-diet-induces-mitochondrial-uncoupling-and-mitochondrial-unfolded-protein-response-in-epididymal-white-adipose-tissue-of-mice
#6
Shylesh Bhaskaran, Archana Unnikrishnan, Rojina Ranjit, Rizwan Qaisar, Gavin Pharaoh, Stephanie Matyi, Michael Kinter, Sathyaseelan S Deepa
White adipose tissue (WAT) mitochondrial dysfunction is linked to the pathogenesis of obesity driven insulin resistance. Dietary conditions that alter fat mass are known to affect white adipocyte mitochondrial function, however, the impact of high calorie diets on white adipocyte mitochondria is not fully understood. The aim of this study is to assess the effect of a diet rich in saturated or polyunsaturated fat on mitochondrial unfolded protein response (UPR(mt)), a retrograde signaling response that maintains mitochondrial homeostasis, in epididymal WAT (eWAT)...
April 26, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28451288/insights-into-clpxp-proteolysis-heterooligomerization-and-partial-deactivation-enhance-chaperone-affinity-and-substrate-turnover-in-listeria-monocytogenes
#7
Dóra Balogh, Maria Dahmen, Matthias Stahl, Marcin Poreba, Malte Gersch, Marcin Drag, Stephan A Sieber
Caseinolytic proteases (ClpP) are important for recognition and controlled degradation of damaged proteins. While the majority of bacterial organisms utilize only a single ClpP, Listeria monocytogenes expresses two isoforms (LmClpP1 and LmClpP2). LmClpPs assemble into either a LmClpP2 homocomplex or a LmClpP1/2 heterooligomeric complex. The heterocomplex in association with the chaperone ClpX, exhibits a boost in proteolytic activity for unknown reasons. Here, we use a combined chemical and biochemical strategy to unravel two activation principles of LmClpPs...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28419231/antibiotic-resistance-in-staphylococcus-aureus-current-status-and-future-prospects
#8
Timothy J Foster
The major targets for antibiotics in staphylococci are (i) the cell envelope, (ii) the ribosome and (iii) nucleic acids. Several novel targets emerged from recent targeted drug discovery programmes including the ClpP protease and FtsZ from the cell division machinery. Resistance can either develop by horizontal transfer of resistance determinants encoded by mobile genetic elements viz plasmids, transposons and the staphylococcal cassette chromosome or by mutations in chromosomal genes. Horizontally acquired resistance can occur by one of the following mechanisms: (i) enzymatic drug modification and inactivation, (ii) enzymatic modification of the drug binding site, (iii) drug efflux, (iv) bypass mechanisms involving acquisition of a novel drug-resistant target, (v) displacement of the drug to protect the target...
May 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28333276/genetic-evidence-that-multiple-proteases-are-involved-in-modulation-of-heat-induced-activation-of-the-sigma-factor-sigi-in-bacillus-subtilis
#9
Tai-Yen Liu, Shu-Hung Chu, Yi-Nei Hu, Jyun-Jhih Wang, Gwo-Chyuan Shaw
The Bacillus subtilis sigI-rsgI operon encodes the heat-inducible sigma factor SigI and its cognate anti-sigma factor RsgI. The heat-activated SigI positively regulates expression of sigI itself and genes involved in cell wall homeostasis and heat resistance. It remains unknown which protease(s) may contribute to degradation of RsgI and heat-induced activation of SigI. In this study, we found that transcription of sigI from its σI-dependent promoter under heat stress was downregulated in a strain lacking the heat-inducible sigma factor SigB...
April 1, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28263850/laser-capture-micro-dissection-combined-with-next-generation-sequencing-analysis-of-cell-type-specific-deafness-gene-expression-in-the-mouse-cochlea
#10
Shin-Ya Nishio, Yutaka Takumi, Shin-Ichi Usami
Cochlear implantation (CI), which directly stimulates the cochlear nerves, is the most effective and widely used medical intervention for patients with severe to profound sensorineural hearing loss. The etiology of the hearing loss is speculated to have a major influence of CI outcomes, particularly in cases resulting from mutations in genes preferentially expressed in the spiral ganglion region. To elucidate precise gene expression levels in each part of the cochlea, we performed laser-capture micro dissection in combination with next-generation sequencing analysis and determined the expression levels of all known deafness-associated genes in the organ of Corti, spiral ganglion, lateral wall, and spiral limbs...
May 2017: Hearing Research
https://www.readbyqxmd.com/read/28186774/quantitative-map-of-%C3%AE-lactone-induced-virulence-regulation
#11
Joanna Krysiak, Matthias Stahl, Jan Vomacka, Christian Fetzer, Markus Lakemeyer, Anja Fux, Stephan A Sieber
β-Lactones have recently been introduced as the first selective ClpP inhibitors that attenuate virulence of both sensitive Staphylococcus aureus and multiresistant strains (MRSA). Although previous knockout studies showed that ClpP is essential for S. aureus alpha-toxin production, a link between β-lactone inhibition and molecular virulence mechanisms has been lacking so far. We here perform a chemical-proteomic approach to elucidate antivirulence pathways. First, we demonstrate by gel-free activity-based protein profiling that ClpP is the predominant target of β-lactones...
February 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28178980/novel-neuro-audiological-findings-and-further-evidence-for-twnk-involvement-in-perrault-syndrome
#12
Monika Ołdak, Dominika Oziębło, Agnieszka Pollak, Iwona Stępniak, Michal Lazniewski, Urszula Lechowicz, Krzysztof Kochanek, Mariusz Furmanek, Grażyna Tacikowska, Dariusz Plewczynski, Tomasz Wolak, Rafał Płoski, Henryk Skarżyński
BACKGROUND: Hearing loss and ovarian dysfunction are key features of Perrault syndrome (PRLTS) but the clinical and pathophysiological features of hearing impairment in PRLTS individuals have not been addressed. Mutations in one of five different genes HSD17B4, HARS2, LARS2, CLPP or TWNK (previous symbol C10orf2) cause the autosomal recessive disorder but they are found only in about half of the patients. METHODS: We report on two siblings with a clinical picture resembling a severe, neurological type of PRLTS...
February 8, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28178222/complete-chloroplast-genome-of-medicinal-plant-lonicera-japonica-genome-rearrangement-intron-gain-and-loss-and-implications-for-phylogenetic-studies
#13
Liu He, Jun Qian, Xiwen Li, Zhiying Sun, Xiaolan Xu, Shilin Chen
The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L...
February 7, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28170446/community-level-physiological-profiling-analyses-show-potential-to-identify-the-copiotrophic-bacteria-present-in-soil-environments
#14
Salvador Lladó, Petr Baldrian
Community-level physiological profiling (CLPP) analyses from very diverse environments are frequently used with the aim of characterizing the metabolic versatility of whole environmental bacterial communities. While the limitations of the methodology for the characterization of whole communities are well known, we propose that CLPP combined with high-throughput sequencing and qPCR can be utilized to identify the copiotrophic, fast-growing fraction of the bacterial community of soil environments, where oligotrophic taxa are usually dominant...
2017: PloS One
https://www.readbyqxmd.com/read/28114338/proteolysis-dependent-remodeling-of-the-tubulin-homolog-ftsz-at-the-division-septum-in-escherichia-coli
#15
Marissa G Viola, Christopher J LaBreck, Joseph Conti, Jodi L Camberg
During bacterial cell division a dynamic protein structure called the Z-ring assembles at the septum. The major protein in the Z-ring in Escherichia coli is FtsZ, a tubulin homolog that polymerizes with GTP. FtsZ is degraded by the two-component ATP-dependent protease ClpXP. Two regions of FtsZ, located outside of the polymerization domain in the unstructured linker and at the C-terminus, are important for specific recognition and degradation by ClpXP. We engineered a synthetic substrate containing green fluorescent protein (Gfp) fused to an extended FtsZ C-terminal tail (residues 317-383), including the unstructured linker and the C-terminal conserved region, but not the polymerization domain, and showed that it is sufficient to target a non-native substrate for degradation in vitro...
2017: PloS One
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#16
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28098783/the-influence-of-the-toxin-antitoxin-mazef-on-growth-and-survival-of-listeria-monocytogenes-under-stress
#17
Thomas D Curtis, Ippei Takeuchi, Lone Gram, Gitte M Knudsen
A major factor in the resilience of Listeria monocytogenes is the alternative sigma factor B (σ(B)). Type II Toxin/Antitoxin (TA) systems are also known to have a role in the bacterial stress response upon activation via the ClpP or Lon proteases. Directly upstream of the σ(B) operon in L. monocytogenes is the TA system mazEF, which can cleave mRNA at UACMU sites. In this study, we showed that the mazEF TA locus does not affect the level of persister formation during treatment with antibiotics in lethal doses, but exerts different effects according to the sub-inhibitory stress added...
January 13, 2017: Toxins
https://www.readbyqxmd.com/read/28061786/attenuated-actinobacillus-pleuropneumoniae-double-deletion-mutant-s-8%C3%A2-clpp-apxiic-confers-protection-against-homologous-or-heterologous-strain-challenge
#18
RANDOMIZED CONTROLLED TRIAL
Fang Xie, Gang Li, Long Zhou, Yanhe Zhang, Ning Cui, Siguo Liu, Chunlai Wang
BACKGROUND: Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, which leads to large economic losses to the swine industry worldwide. In this study, S-8△clpP△apxIIC, a double-deletion mutant of A. pleuropneumoniae was constructed, and its safety and protective efficacy were evaluated in pigs. RESULTS: The S-8△clpP△apxIIC mutant exhibited attenuated virulence in a murine (BALB/c) model, and caused no detrimental effects on pigs even at a dose of up to 1...
January 6, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28049149/rela-mutant-enterococcus-faecium-with-multiantibiotic-tolerance-arising-in-an-immunocompromised-host
#19
Erin S Honsa, Vaughn S Cooper, Mohammed N Mhaissen, Matthew Frank, Jessica Shaker, Amy Iverson, Jeffrey Rubnitz, Randall T Hayden, Richard E Lee, Charles O Rock, Elaine I Tuomanen, Joshua Wolf, Jason W Rosch
Serious bacterial infections in immunocompromised patients require highly effective antibacterial therapy for cure, and thus, this setting may reveal novel mechanisms by which bacteria circumvent antibiotics in the absence of immune pressure. Here, an infant with leukemia developed vancomycin-resistant Enterococcus faecium (VRE) bacteremia that persisted for 26 days despite appropriate antibiotic therapy. Sequencing of 22 consecutive VRE isolates identified the emergence of a single missense mutation (L152F) in relA, which constitutively activated the stringent response, resulting in elevated baseline levels of the alarmone guanosine tetraphosphate (ppGpp)...
January 3, 2017: MBio
https://www.readbyqxmd.com/read/28011364/functionality-of-microbial-communities-in-constructed-wetlands-used-for-pesticide-remediation-influence-of-system-design-and-sampling-strategy
#20
Tao Lv, Pedro N Carvalho, Liang Zhang, Yang Zhang, Mark Button, Carlos A Arias, Kela P Weber, Hans Brix
The objective of this study was to compare the microbial community metabolic function from both unsaturated and saturated constructed wetland mesocosms (CWs) when treating the pesticide tebuconazole. The comparison was performed for both interstitial water and substrate biofilm by community level physiological profiling (CLPP) via BIOLOG™ EcoPlates. For each CW design (saturated or unsaturated), six mesocosms were established including one unplanted and five planted individually with either Juncus effusus, Typha latifolia, Berula erecta, Phragmites australis or Iris pseudacorus...
March 1, 2017: Water Research
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