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https://www.readbyqxmd.com/read/29183996/structural-characterization-of-the-bacterial-proteasome-homolog-bph-reveals-a-tetradecameric-double-ring-complex-with-unique-inner-cavity-properties
#1
Adrian C D Fuchs, Lorena Maldoner, Katharina Hipp, Marcus D Hartmann, Jörg Martin
Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires the interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ ATPase HslU; the ClpP protease with its partner AAA+ ATPase ClpX; and Anbu, a recently characterized ancestral proteasome variant...
November 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29137643/efficient-gene-editing-in-corynebacterium-glutamicum-using-the-crispr-cas9-system
#2
Feng Peng, Xinyue Wang, Yang Sun, Guibin Dong, Yankun Yang, Xiuxia Liu, Zhonghu Bai
BACKGROUND: Corynebacterium glutamicum (C. glutamicum) has traditionally been used as a microbial cell factory for the industrial production of many amino acids and other industrially important commodities. C. glutamicum has recently been established as a host for recombinant protein expression; however, some intrinsic disadvantages could be improved by genetic modification. Gene editing techniques, such as deletion, insertion, or replacement, are important tools for modifying chromosomes...
November 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29109185/genome-wide-screens-reveal-new-gene-products-that-influence-genetic-competence-in-streptococcus-mutans
#3
Robert C Shields, Greg O'Brien, Natalie Maricic, Alexandria Kesterson, Megan Grace, Stephen J Hagen, Robert A Burne
A network of genes and at least two peptide signaling molecules tightly control when Streptococcus mutans becomes competent to take up DNA from its environment. Widespread changes in the expression of genes occur when S. mutans is presented with competence signal peptides in vitro, including increased production of the alternative sigma factor, ComX, which activates late competence genes. Still, the way that gene products that are regulated by competence peptides influence DNA uptake and cellular physiology are not well understood...
November 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28924169/the-clpxp-protease-is-dispensable-for-degradation-of-unfolded-proteins-in-staphylococcus-aureus
#4
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/28906057/a-chemical-disruptor-of-the-clpx-chaperone-complex-attenuates-the-virulence-of-multidrug-resistant-staphylococcus-aureus
#5
Christian Fetzer, Vadim S Korotkov, Robert Thänert, Kyu Myung Lee, Martin Neuenschwander, Jens Peter von Kries, Eva Medina, Stephan A Sieber
The Staphylococcus aureus ClpXP protease is an important regulator of cell homeostasis and virulence. We utilized a high-throughput screen against the ClpXP complex and identified a specific inhibitor of the ClpX chaperone that disrupts its oligomeric state. Synthesis of 34 derivatives revealed that the molecular scaffold is restrictive for diversification, with only minor changes tolerated. Subsequent analysis of the most active compound revealed strong attenuation of S. aureus toxin production, which was quantified with a customized MS-based assay platform...
September 14, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28884668/borrelia-lanei-sp-nov-extends-the-diversity-of-borrelia-species-in-california
#6
Gabriele Margos, Natalia Fedorova, Joyce E Kleinjan, Christine Hartberger, Tom G Schwan, Andreas Sing, Volker Fingerle
The diversity of Borrelia species discovered in California appears to be particularly high. A divergent group of Borrelia strains collected from Ixodes ticks in California was described by Postic and co-workers and designated 'genomospecies 2' (Postic D, Garnier M, Baranton G. Int J Med Microbiol 2007;297:263-271; Postic D, Ras NM, Lane RS, Hendson M, Baranton G. J Clin Microbiol 1998;36:3497-3504). We performed multilocus sequence analysis (MLSA) using eight housekeeping loci (clpA, clpX, nifS, pepX, pyrG, recG, rplB and uvrA) on 12 strains of this Borreliagenospecies to confirm that these strains form a distinct group within the Borreliaburgdorferi s...
October 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28874591/mutation-in-human-clpx-elevates-levels-of-%C3%AE-aminolevulinate-synthase-and-protoporphyrin-ix-to-promote-erythropoietic-protoporphyria
#7
Yvette Y Yien, Sarah Ducamp, Lisa N van der Vorm, Julia R Kardon, Hana Manceau, Caroline Kannengiesser, Hector A Bergonia, Martin D Kafina, Zoubida Karim, Laurent Gouya, Tania A Baker, Hervé Puy, John D Phillips, Gaël Nicolas, Barry H Paw
Loss-of-function mutations in genes for heme biosynthetic enzymes can give rise to congenital porphyrias, eight forms of which have been described. The genetic penetrance of the porphyrias is clinically variable, underscoring the role of additional causative, contributing, and modifier genes. We previously discovered that the mitochondrial AAA+ unfoldase ClpX promotes heme biosynthesis by activation of δ-aminolevulinate synthase (ALAS), which catalyzes the first step of heme synthesis. CLPX has also been reported to mediate heme-induced turnover of ALAS...
September 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28814717/drosophila-protease-clpxp-specifically-degrades-dmlrpprc1-controlling-mitochondrial-mrna-and-translation
#8
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/28795723/intracellular-iron-and-heme-trafficking-and-metabolism-in-developing-erythroblasts
#9
Martin D Kafina, Barry H Paw
Vertebrate red blood cells (RBCs) arise from erythroblasts in the human bone marrow through a process known as erythropoiesis. Iron uptake is a crucial hallmark, essential for heme biosynthesis in the differentiating erythroblasts, which are dedicated to producing hemoglobin. Erythropoiesis is facilitated by a network of intracellular transport proteins, chaperones, and circulating hormones. Intracellular iron is targeted to the mitochondria for incorporation into a porphyrin ring to form heme and cytosolic iron-sulfur proteins, including Iron Regulatory Protein 1 (IRP1)...
September 20, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28717043/tandem-amplification-of-the-staphylococcal-cassette-chromosome-mec-element-can-drive-high-level-methicillin-resistance-in-methicillin-resistant-staphylococcus-aureus
#10
Laura A Gallagher, Simone Coughlan, Nikki S Black, Pierce Lalor, Elaine M Waters, Bryan Wee, Mick Watson, Tim Downing, J Ross Fitzgerald, Gerard T A Fleming, James P O'Gara
Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) strains typically express high-level, homogeneous (HoR) β-lactam resistance, whereas community-associated MRSA (CA-MRSA) more commonly express low-level heterogeneous (HeR) resistance. Expression of the HoR phenotype typically requires both increased expression of the mecA gene, carried on the staphylococcal cassette chromosome mec element (SCCmec), and additional mutational event(s) elsewhere on the chromosome. Here the oxacillin concentration in a chemostat culture of the CA-MRSA strain USA300 was increased from 8 μg/ml to 130 μg/ml over 13 days to isolate highly oxacillin-resistant derivatives...
September 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28659890/pre-cultivation-with-selected-prebiotics-enhances-the-survival-and-the-stress-response-of-lactobacillus-rhamnosus-strains-in-simulated-gastrointestinal-transit
#11
Mariantonietta Succi, Patrizio Tremonte, Gianfranco Pannella, Luca Tipaldi, Autilia Cozzolino, Rossana Romaniello, Elena Sorrentino, Raffaele Coppola
In our study, we dwelled upon combinations of lactobacilli/prebiotics, considering four different strains belonging to the Lactobacillus rhamnosus species, including Lactobacillus rhamnosus GG (LGG), and different prebiotics often found in commercial synbiotic products, such as inulin, lactulose and polyols mannitol and sorbitol. In the first step of the research, the survival, the growth kinetic parameters and the protein expression of Lb. rhamnosus strains cultivated in presence of the different prebiotics as a unique carbon source were evaluated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28536693/the-essential-role-of-clpxp-in-caulobacter-crescentus-requires-species-constrained-substrate-specificity
#12
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
#13
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/28490437/high-throughput-crispri-phenotyping-identifies-new-essential-genes-in-streptococcus-pneumoniae
#14
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/28467184/multilocus-genetic-characterization-of-lactobacillus-fermentum-isolated-from-ready-to-eat-canned-food
#15
Irshad M Sulaiman, Emily Jacobs, Steven Simpson, Khalil Kerdahi
The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa...
June 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28451288/insights-into-clpxp-proteolysis-heterooligomerization-and-partial-deactivation-enhance-chaperone-affinity-and-substrate-turnover-in-listeria-monocytogenes
#16
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/28421184/the-proteasomal-atpases-use-a-slow-but-highly-processive-strategy-to-unfold-proteins
#17
Aaron Snoberger, Raymond T Anderson, David M Smith
All domains of life have ATP-dependent compartmentalized proteases that sequester their peptidase sites on their interior. ATPase complexes will often associate with these compartmentalized proteases in order to unfold and inject substrates into the protease for degradation. Significant effort has been put into understanding how ATP hydrolysis is used to apply force to proteins and cause them to unfold. The unfolding kinetics of the bacterial ATPase, ClpX, have been shown to resemble a fast motor that traps unfolded intermediates as a strategy to unfold proteins...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28186774/quantitative-map-of-%C3%AE-lactone-induced-virulence-regulation
#18
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...
March 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28114338/proteolysis-dependent-remodeling-of-the-tubulin-homolog-ftsz-at-the-division-septum-in-escherichia-coli
#19
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/28112428/specific-glutamic-acid-residues-in-targeted-proteins-induce-exaggerated-retardations-in-phos-tag-sds-page-migration
#20
Eiji Kinoshita, Emiko Kinoshita-Kikuta, Kiyonobu Karata, Toshiki Kawano, Atsuhiro Nishiyama, Morihisa Yamato, Tohru Koike
We describe two unique proteins, Escherichia coli ClpX and human histone H2A, that show extremely retarded migrations relative to their molecular weights in Phos-tag SDS-PAGE, despite being nonphosphorylated. Although ClpX separated into multiple migration bands in Phos-tag gels, the separation was not due to phosphorylation. The N-terminal 47-61 region of ClpX was responsible for producing multiple phosphorylation-independent structural variants, even under denaturing conditions, and some of these variants were detected as highly up-shifted bands...
April 2017: Electrophoresis
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