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https://www.readbyqxmd.com/read/28731202/on-the-brink-the-highly-reduced-plastomes-of-nonphotosynthetic-ericaceae
#1
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
#2
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
#3
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...
July 8, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28681284/microbial-biodiversity-of-meadows-under-different-modes-of-land-use-catabolic-and-genetic-fingerprinting
#4
Agnieszka Wolinska, Magdalena Frąc, Karolina Oszust, Anna Szafranek-Nakonieczna, Urszula Zielenkiewicz, Zofia Stępniewska
The main goal of the study was to find differences in the bacterial community structure resulting from different ways of meadow management in order to get the first insight into microbial biodiversity in meadow samples. The next generation sequencing technique (454-pyrosequencing) was accompanied with the community level physiological profiling (CLPP) method in order to acquire combined knowledge of both genetic and catabolic bacterial fingerprinting of two studied meadows (hayland and pasture). Soil samples (FAO: Mollic Gleysol) were taken in April 2015 from the surface layer (0-20 cm)...
August 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28674070/bacillus-subtilis-intramembrane-protease-rasp-activity-in-escherichia-coli-and-in-vitro
#5
Daniel Parrell, Yang Zhang, Sandra Olenic, Lee Kroos
RasP is a predicted intramembrane metalloprotease of Bacillus subtilis that has been proposed to cleave the stress response anti-sigma factors RsiW and RsiV, the cell division protein FtsL, and remnant signal peptides, within their transmembrane segments. To provide evidence for direct effects of RasP on putative substrates, we developed a heterologous coexpression system. Since expression of catalytically-inactive RasP E21A inhibited expression of other membrane proteins in Escherichia coli, we added extra transmembrane segments to RasP E21A, which allowed accumulation of most other membrane proteins...
July 3, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28666467/the-metabolic-footprint-of-the-airway-bacterial-community-in-cystic-fibrosis
#6
Vaishnavi Narayanamurthy, John M Sweetnam, Darcy R Denner, Lena W Chen, Edward T Naureckas, Bharathi Laxman, Steven R White
BACKGROUND: Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF...
June 30, 2017: Microbiome
https://www.readbyqxmd.com/read/28629725/relationship-between-histopathological-status-of-the-helicobacter-pylori-infected-patients-and-proteases-of-h-%C3%A2-pylori-in-isolates-carrying-diverse-virulence-genotypes
#7
Somayyeh Gharibi, Tahereh Falsafi, Masoud Alebouyeh, Nastaran Farzi, Farzam Vaziri, Mohamad Reza Zali
Helicobacter pylori is the main cause of several gastroduodenal diseases in Humans. Among various virulence factors of H. pylori, proteases may also be involved in its pathogenicity. In this study, relationship between proteolytic activity of H. pylori strains and histopathological changes of the stomach was investigated in the patients infected with strains carrying diverse virulence factors. H. pylori strains were isolated from the biopsies of 116 patients who referred to hospital for their gastroduodenal disorders, in Tehran, Iran...
June 16, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28625996/natural-dna-transformation-is-functional-in-lactococcus-lactis-ssp-cremoris-kw2
#8
Blandine David, Amandine Radziejwoski, Frédéric Toussaint, Laetitia Fontaine, Marie Henry de Frahan, Cédric Patout, Sabine van Dillen, Patrick Boyaval, Philippe Horvath, Christophe Fremaux, Pascal Hols
Lactococcus lactis is one of the most commonly used lactic acid bacteria in the dairy industry. Activation of competence for natural DNA transformation in this species would greatly improve the selection of novel strains with desired genetic traits. Here, we investigated the activation of natural transformation in L. lactis ssp. cremoris KW2, a strain of plant origin whose genome encodes the master competence regulator ComX and the complete set of proteins usually required for natural transformation. In the absence of knowledge about competence regulation in this species, we constitutively overproduced ComX in a reporter strain of late competence phase activation and showed, by transcriptomic analyses, a ComX-dependent induction of all key competence genes...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28619145/thymol-kills-bacteria-reduces-biofilm-formation-and-protects-mice-against-a-fatal-infection-of-actinobacillus-pleuropneumoniae-strain-l20
#9
Lei Wang, Xueqin Zhao, Chunling Zhu, Xiaojing Xia, Wanhai Qin, Mei Li, Tongzhao Wang, Shijun Chen, Yanzhao Xu, Bolin Hang, Yawei Sun, Jinqing Jiang, Langford Paul Richard, Liancheng Lei, Gaiping Zhang, Jianhe Hu
Actinobacillus pleuropneumoniae is the causative agent of the highly contagious and deadly respiratory infection porcine pleuropneumonia, resulting in serious losses to the pig industry worldwide. Alternative to antibiotics are urgently needed due to the serious increase in antimicrobial resistance. Thymol is a monoterpene phenol and efficiently kills a variety of bacteria. This study found that thymol has strong bactericidal effects on the A. pleuropneumoniae 5b serotype strain, an epidemic strain in China...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28617867/complete-chloroplast-genome-sequence-of-common-bermudagrass-cynodon-dactylon-l-pers-and-comparative-analysis-within-the-family-poaceae
#10
Ya-Yi Huang, Shu-Ting Cho, Mindia Haryono, Chih-Horng Kuo
Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp)...
2017: PloS One
https://www.readbyqxmd.com/read/28585016/ecotoxicological-assessment-of-pesticides-and-their-combination-on-rhizospheric-microbial-community-structure-and-function-of-vigna-radiata
#11
Varsha Ashok Walvekar, Swati Bajaj, Dileep K Singh, Shilpi Sharma
India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata...
July 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28555174/the-atp-dependent-protease-clpp-inhibits-biofilm-formation-by-regulating-agr-and-cell-wall-hydrolase-sle1-in-staphylococcus-aureus
#12
Qian Liu, Xing Wang, Juanxiu Qin, Sen Cheng, Won-Sik Yeo, Lei He, Xiaowei Ma, Xiaoyun Liu, Min Li, Taeok Bae
Biofilm causes hospital-associated infections on indwelling medical devices. In Staphylococcus aureus, Biofilm formation is controlled by intricately coordinated network of regulating systems, of which the ATP-dependent protease ClpP shows an inhibitory effect. Here, we demonstrate that the inhibitory effect of ClpP on biofilm formation is through Agr and the cell wall hydrolase Sle1. Biofilm formed by clpP mutant consists of proteins and extracellular DNA (eDNA). The increase of the protein was, at least in part, due to the reduced protease activity of the mutant, which was caused by the decreased activity of agr...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28536693/the-essential-role-of-clpxp-in-caulobacter-crescentus-requires-species-constrained-substrate-specificity
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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