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https://www.readbyqxmd.com/read/29129755/phylogenetic-analysis-predicts-structural-divergence-for-proteobacterial-clpc-proteins
#1
Justin M Miller, Hamza Chaudhary, Justin D Marsee
Regulated proteolysis is required in all organisms for the removal of misfolded or degradation-tagged protein substrates in cellular quality control pathways. The molecular machines that catalyze this process are known as ATP-dependent proteases with examples that include ClpAP and ClpCP. Clp/Hsp100 subunits form ring-structures that couple the energy of ATP binding and hydrolysis to protein unfolding and subsequent translocation of denatured protein into the compartmentalized ClpP protease for degradation...
November 9, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29117582/rational-dose-of-insecticide-chlorantraniliprole-displays-a-transient-impact-on-the-microbial-metabolic-functions-and-bacterial-community-in-a-silty-loam-paddy-soil
#2
Meng Wu, Guilong Li, Xiaofen Chen, Jia Liu, Ming Liu, Chunyu Jiang, Zhongpei Li
Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There have been few studies regarding its effects on soil microbial functional diversity and bacterial community composition. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP under different application doses in a silty-loam paddy soil in subtropical China. The half-life of CAP was 51.3 and 62.5d for low (1mgkg(-1)) and high (10mgkg(-1)) application dose, respectively. We used a combination of community level physiological profile (CLPP) and 16S rRNA gene sequencing analysis to get insights into the soil microbial features responded to CAP during the experiment...
November 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29095905/the-complete-chloroplast-genome-sequence-of-the-cam-epiphyte-spanish-moss-tillandsia-usneoides-bromeliaceae-and-its-comparative-analysis
#3
Péter Poczai, Jaakko Hyvönen
Spanish moss (Tillandsia usneoides) is an epiphytic bromeliad widely distributed throughout tropical and warm temperate America. This plant is highly adapted to extreme environmental conditions. Striking features of this species include specialized trichomes (scales) covering the surface of its shoots aiding the absorption of water and nutrients directly from the atmosphere and a specific photosynthesis using crassulacean acid metabolism (CAM). Here we report the plastid genome of Spanish moss and present the comparison of genome organization and sequence evolution within Poales...
2017: PloS One
https://www.readbyqxmd.com/read/29053825/pdm3-a-pentatricopeptide-repeat-containing-protein-affects-chloroplast-development
#4
Jian Zhang, Jianwei Xiao, Yuqian Li, Bodan Su, Huimin Xu, Xiaoyi Shan, Chengwei Song, Jianbo Xie, Ruili Li
The chloroplast, as the photosynthetic organelle of plants, plays a crucial role in plant development. Extensive studies have been conducted on chloroplast development; however, the related regulatory mechanism still remains elusive. Here, we characterized a mutant with defective chloroplasts in Arabidopsis, termed pigment-defective mutant3 (pdm3), which exhibits a distinct albino phenotype in leaves, eventually leading to pdm3 seedling lethality under autotrophic growth conditions. Electron microscopy demonstrated that the number of thylakoids was reduced and the structure of those thylakoids was disrupted in the pdm3 mutant, which eventually led to the breakdown of chloroplasts...
October 19, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29046685/comparative-analysis-of-the-complete-plastomes-of-apostasia-wallichii-and-neuwiedia-singapureana-apostasioideae-reveals-different-evolutionary-dynamics-of-ir-ssc-boundary-among-photosynthetic-orchids
#5
Zhitao Niu, Jiajia Pan, Shuying Zhu, Ludan Li, Qingyun Xue, Wei Liu, Xiaoyu Ding
Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29031699/a-genetic-tool-to-quantify-trans-translation-activity-in-vivo
#6
Kevin Macé, Fanny Demay, Charlotte Guyomar, Sylvie Georgeault, Emmanuel Giudice, Renan Goude, Annie Trautwetter, Gwennola Ermel, Carlos Blanco, Reynald Gillet
In bacteria, trans-translation is the main quality control mechanism for rescuing ribosomes arrested during translation. This key process is universally conserved and plays a critical role in the viability and virulence of many pathogens. We developed a reliable in vivo double-fluorescence reporter system for the simultaneous quantification of both trans-translation and the associated proteolysis activities in bacteria. The assay was validated using mutant bacteria lacking tmRNA, SmpB, and the ClpP protease...
October 13, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28924169/the-clpxp-protease-is-dispensable-for-degradation-of-unfolded-proteins-in-staphylococcus-aureus
#7
Steen G Stahlhut, Abdulelah A Alqarzaee, Camilla Jensen, Niclas S Fisker, Ana R Pereira, Mariana G Pinho, Vinai Chittezham Thomas, Dorte Frees
In living cells intracellular proteolysis is crucial for protein homeostasis, and ClpP proteases are conserved between eubacteria and the organelles of eukaryotic cells. In Staphylococcus aureus, ClpP associates to the substrate specificity factors, ClpX and ClpC forming two ClpP proteases, ClpXP and ClpCP. To address how individual ClpP proteases impact cell physiology, we constructed a S. aureus mutant expressing ClpX with an I265E substitution in the ClpP recognition tripeptide of ClpX. This mutant cannot degrade established ClpXP substrates confirming that the introduced amino acid substitution abolishes ClpXP activity...
September 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28922556/structure-and-mechanism-of-the-monoterpene-cyclolavandulyl-diphosphate-synthase-that-catalyzes-consecutive-condensation-and-cyclization
#8
Takeo Tomita, Masaya Kobayashi, Yuma Karita, Yoko Yasuno, Tetsuro Shinada, Makoto Nishiyama, Tomohisa Kuzuyama
We report the three-dimensional structure of cyclolavandulyl diphosphate (CLPP) synthase (CLDS), which consecutively catalyzes the condensation of two molecules of dimethylallyl diphosphate (DMAPP) followed by cyclization to form a cyclic monoterpene, CLPP. The structures of apo-CLDS and CLDS in complex with Tris, pyrophosphate, and Mg(2+) ion were refined at 2.00 Å resolution and 1.73 Å resolution, respectively. CLDS adopts a typical fold for cis-prenyl synthases and forms a homo-dimeric structure. An in vitro reaction using a regiospecifically (2) H-substituted DMAPP substrate revealed the intramolecular proton transfer mechanism of the CLDS reaction...
September 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28917450/a-novel-class-of-plasmodial-clpp-protease-inhibitors-as-potential-antimalarial-agents
#9
Sourabh Mundra, Vandana Thakur, Angelica M Bello, Sumit Rathore, Mohd Asad, Lianhu Wei, Jane Yang, Sai Kumar Chakka, Radhakrishnan Mahesh, Pawan Malhotra, Asif Mohmmed, Lakshmi P Kotra
The prokaryotic ATP-dependent ClpP protease, localized in the relict plastid of malaria parasite, represents a potential drug target. In the present study, we utilized in silico structure-based screening and medicinal chemistry approaches to identify a novel pyrimidine series of compounds inhibiting P. falciparum ClpP protease activity and evaluated their antiparasitic activities. Structure-activity relationship indicated that morpholine moiety at C2, an aromatic substitution at N3 and a 4-oxo moiety on the pyrimidine are important for potent inhibition of ClpP enzyme along with antiparasiticidal activity...
September 5, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28910721/an-amino-acid-domino-effect-orchestrates-clpp-s-conformational-states
#10
REVIEW
Matthias Stahl, Stephan A Sieber
Maintaining the cellular protein homeostasis means managing life on the brink of death. This balance is largely based on precise fine-tuning of enzyme activities. For instance, the ClpP protease possesses several conformational switches which are fundamental to regulating its activity. Efforts have focused on revealing the structural basis of ClpP's conformational control. In the last decade, several amino acid clusters have been identified and functionally linked to specific activation states. Researchers have now begun to couple these hotspots to one another, uncovering a global network of residues that switch in response to internal and external stimuli...
September 11, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28882736/gene-centric-metegenome-analysis-reveals-diversity-of-pseudomonas-aeruginosa-biofilm-gene-orthologs-in-fresh-water-ecosystem
#11
Rani Anupama, Amitava Mukherjee, Subramanian Babu
Metagenomic analysis of biofilm forming bacteria in environmental samples remains challenging due to the non-availability of gene sequences of most of the uncultivable bacteria. Sequences of Pseudomonas aeruginosa PAO1-UW genes involved either directly or indirectly in biofilm formation were analyzed using BLASTn to obtain matching sequences from different strain, species and genus. Conserved regions in the functional domain of the amino acid sequences were used to design common primers for direct PCR analysis of freshwater metagenomes...
September 4, 2017: Genomics
https://www.readbyqxmd.com/read/28854633/contrasting-patterns-of-nucleotide-substitution-rates-provide-insight-into-dynamic-evolution-of-plastid-and-mitochondrial-genomes-of-geranium
#12
Seongjun Park, Tracey A Ruhlman, Mao-Lun Weng, Nahid H Hajrah, Jamal S M Sabir, Robert K Jansen
Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28814717/drosophila-protease-clpxp-specifically-degrades-dmlrpprc1-controlling-mitochondrial-mrna-and-translation
#13
Yuichi Matsushima, Yuta Hirofuji, Masamune Aihara, Song Yue, Takeshi Uchiumi, Laurie S Kaguni, Dongchon Kang
ClpXP is the major protease in the mitochondrial matrix in eukaryotes, and is well conserved among species. ClpXP is composed of a proteolytic subunit, ClpP, and a chaperone-like subunit, ClpX. Although it has been proposed that ClpXP is required for the mitochondrial unfolded protein response, additional roles for ClpXP in mitochondrial biogenesis are unclear. Here, we found that Drosophila leucine-rich pentatricopeptide repeat domain-containing protein 1 (DmLRPPRC1) is a specific substrate of ClpXP. Depletion or introduction of catalytically inactive mutation of ClpP increases DmLRPPRC1 and causes non-uniform increases of mitochondrial mRNAs, accumulation of some unprocessed mitochondrial transcripts, and modest repression of mitochondrial translation in Drosophila Schneider S2 cells...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800729/accd-nuclear-transfer-of-platycodon-grandiflorum-and-the-plastid-of-early-campanulaceae
#14
Chang Pyo Hong, Jihye Park, Yi Lee, Minjee Lee, Sin Gi Park, Yurry Uhm, Jungho Lee, Chang-Kug Kim
BACKGROUND: Campanulaceae species are known to have highly rearranged plastid genomes lacking the acetyl-CoA carboxylase (ACC) subunit D gene (accD), and instead have a nuclear (nr)-accD. Plastid genome information has been thought to depend on studies concerning Trachelium caeruleum and genome announcements for Adenophora remotiflora, Campanula takesimana, and Hanabusaya asiatica. RNA editing information for plastid genes is currently unavailable for Campanulaceae. To understand plastid genome evolution in Campanulaceae, we have sequenced and characterized the chloroplast (cp) genome and nr-accD of Platycodon grandiflorum, a basal member of Campanulaceae...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28799020/from-discovery-of-the-chop-axis-and-targeting-clpp-to-the-identification-of-additional-axes-of-the-uprmt-driven-by-the-estrogen-receptor-and-sirt3
#15
Timothy C Kenny, Doris Germain
The mitochondrial UPR (UPR(mt)) is rapidly gaining attention. While most studies on the UPR(mt) have focused on its role in aging, emerging studies suggest an important role of the UPR(mt) in cancer. Further, several of the players of the UPR(mt) in mammalian cells have well reported roles in the maintenance of the organelle. The goal of this review is to emphasize aspects of the UPR(mt) that have been overlooked in the current literature, describe the role of specific players of the UPR(mt) in the biology of the mitochondria and highlight the intriguing possibility that targeting the UPR(mt) in cancer may be already within reach...
August 2017: Journal of Bioenergetics and Biomembranes
https://www.readbyqxmd.com/read/28751741/soil-microbial-community-structure-and-catabolic-activity-are-significantly-degenerated-in-successive-rotations-of-chinese-fir-plantations
#16
Zeyan Wu, Jianjuan Li, Jie Zheng, Jinfu Liu, Shuying Liu, Wenxiong Lin, Chengzhen Wu
This study examined the hypotheses that soil microbial community composition and catabolic activity would significantly degenerated by consecutive monoculture in Chinese fir plantations. The phospholipid fatty acids (PLFA) and community level physiological profiles (CLPP) methods were used to assess the variations of soil microbial community among the first rotation Chinese fir plantation (FCP), the second rotation plantation (SCP) and the third rotation plantation (TCP). The total content of PLFA biomarkers was highest in FCP, followed by SCP, and TCP was the least detected...
July 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28748570/lichen-planopilaris-in-a-latin-american-chilean-population-demographics-clinical-profile-and-treatment-experience
#17
F Mardones, J Shapiro
BACKGROUND: Lichen planopilaris (LPP) is characterized by lymphocytic infiltrate, fibrosis and potential destruction of the hair follicle. Demographic and clinical studies in LPP are limited, and racial differences have not been thoroughly investigated. AIM: To analyse epidemiological data and clinical profiles of Chilean adults with LPP, and report on the treatments used. METHODS: This was a retrospective review of medical records and clinical follow-up of Chilean adults with a clinical and histopathological diagnosis of LPP...
October 2017: Clinical and Experimental Dermatology
https://www.readbyqxmd.com/read/28731202/on-the-brink-the-highly-reduced-plastomes-of-nonphotosynthetic-ericaceae
#18
Thomas W A Braukmann, Michael B Broe, Saša Stefanović, John V Freudenstein
Ericaceae (the heather family) is a large and diverse group of plants that forms elaborate symbiotic relationships with mycorrhizal fungi, and includes several nonphotosynthetic lineages. Using an extensive sample of fully mycoheterotrophic (MH) species, we explored inter- and intraspecific variation as well as selective constraints acting on the plastomes of these unusual plants. The plastomes of seven MH genera were analysed in a phylogenetic context with two geographically disparate individuals sequenced for Allotropa, Monotropa, and Pityopus...
July 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28707598/protein-tagging-destruction-and-infection
#19
Chetana Bhaskarla, Manoj Bhosale, Pip Banerjee, Nagasuma Chandra, Dipankar Nandi
Cells possess protein quality control mechanisms to maintain proper cellular homeostasis. In eukaryotes, the roles of the ubiquitination and proteasome-mediated degradation of cellular proteins is well established. Recent studies have elucidated protein tagging mechanisms in prokaryotes, involving transfer messenger RNA (tmRNA) and pupylation. In this review, newer insights and bioinformatics analysis of two distinct bacterial protein tagging machineries are discussed. The machinery for tmRNA-mediated tagging is present in several eubacterial representatives, e...
July 13, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28698145/increase-in-proteins-involved-in-mitochondrial-fission-mitophagy-proteolysis-and-antioxidant-response-in-type-i-endometrial-cancer-as-an-adaptive-response-to-respiratory-complex-i-deficiency
#20
Antonella Cormio, Clara Musicco, Giuseppe Gasparre, Gennaro Cormio, Vito Pesce, Anna Maria Sardanelli, Maria Nicola Gadaleta
Pathogenic mtDNA mutations associated with alterations of respiratory complex I, mitochondrial proliferation (oncocytic-like phenotype) and increase in antioxidant response were previously reported in type I endometrial carcinoma (EC). To evaluate whether in the presence of pathogenic mtDNA mutations other mitochondrial adaptive processes are triggered by cancer cells, the expression level of proteins involved in mitochondrial dynamics, mitophagy, proteolysis and apoptosis were evaluated in type I ECs harboring pathogenic mtDNA mutations and complex I deficiency...
September 9, 2017: Biochemical and Biophysical Research Communications
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