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https://www.readbyqxmd.com/read/28741612/an-information-theoretic-framework-reveals-a-tunable-allosteric-network-in-group-ii-chaperonins
#1
Tom Lopez, Kevin Dalton, Anthony Tomlinson, Vijay Pande, Judith Frydman
ATP-dependent allosteric regulation of the ring-shaped group II chaperonins remains ill defined, in part because their complex oligomeric topology has limited the success of structural techniques in suggesting allosteric determinants. Further, their high sequence conservation has hindered the prediction of allosteric networks using mathematical covariation approaches. Here, we develop an information theoretic strategy that is robust to residue conservation and apply it to group II chaperonins. We identify a contiguous network of covarying residues that connects all nucleotide-binding pockets within each chaperonin ring...
July 24, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28741466/binding-of-cxcr4-transmembrane-peptides-to-the-bacterial-chaperonin-groel
#2
Xiaoqiang Wang, Haixia Chi, Shixin Li, Yan Xu
: Newly translated membrane protein CXCR4 was observed to gain significant folding enhancement upon interacting with the bacterial chaperonin GroEL-GroES. The main fold of CXCR4 consists of 7 transmembrane α-helices distinct from soluble proteins that have dominated research on the chaperonin-assisted folding. This work extends our previous observation to the binding of GroEL with CXCR4 transmembrane peptides, which are mainly composed of hydrophobic residues characteristic of the substrates recognized by the chaperonin...
July 24, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28731469/novel-chaperonins-are-prevalent-in-the-virioplankton-and-demonstrate-links-to-viral-biology-and-ecology
#3
Rachel L Marine, Daniel J Nasko, Jeffrey Wray, Shawn W Polson, K Eric Wommack
Chaperonins are protein-folding machinery found in all cellular life. Chaperonin genes have been documented within a few viruses, yet, surprisingly, analysis of metagenome sequence data indicated that chaperonin-carrying viruses are common and geographically widespread in marine ecosystems. Also unexpected was the discovery of viral chaperonin sequences related to thermosome proteins of archaea, indicating the presence of virioplankton populations infecting marine archaeal hosts. Virioplankton large subunit chaperonin sequences (GroELs) were divergent from bacterial sequences, indicating that viruses have carried this gene over long evolutionary time...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28713028/the-effect-of-fusarium-culmorum-infection-and-deoxynivalenol-don-application-on-proteome-response-in-barley-cultivars-chevron-and-pedant
#4
Klára Kosová, Jana Chrpová, Jiří Šantrůček, Radovan Hynek, Lenka Štěrbová, Pavel Vítámvás, Jana Bradová, Ilja Tom Prášil
Fusarium head blight (FHB) disease adversely affects grain quality and final yield in small-grain cereals including barley. In the present study, the effect of an artificial infection with Fusarium culmorum and an application of deoxynivalenol (DON) on barley spikes of cultivars Chevron and Pedant during flowering was investigated at grain mid-dough stage (BBCH 73) 10days after pathogen inoculation (10 dai). Proteomic analysis using a two-dimensional differential gel electrophoresis (2D-DIGE) technique coupled with LC-MS/MS investigated 98 protein spots revealing quantitative or qualitative differences between the experimental variants...
July 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28705905/genome-wide-transcriptional-dynamics-in-the-companion-bacterial-symbionts-of-the-glassy-winged-sharpshooter-cicadellidae-homalodisca-vitripennis-reveal-differential-gene-expression-in-bacteria-occupying-multiple-host-organs
#5
Gordon M Bennett, Rebecca A Chong
The agricultural pest the Glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae: GWSS), harbors two bacterial symbionts, "Candidatus Sulcia muelleri" and "Ca Baumannia cicadellinicola", that provide the ten essential amino acids (EAAs) limited in the host plant-sap diet. Although differing in origins and symbiotic age, both bacteria have experienced extensive genome degradation resulting from their ancient restriction to specialized host organs (bacteriomes) that provide cellular support and ensure vertical transmission...
July 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28703007/a-chaperonin-nanocaged-hemin-as-an-artificial-metalloenzyme-for-oxidation-catalysis
#6
Xiaoqiang Wang, Chao Wang, Meihong Pan, Junting Wei, Fuping Jiang, Rongsheng Lu, Xuan Liu, Yihui Huang, Fang Huang
Taking inspiration from biology's effectiveness in functionalizing protein-based nanocages for chemical processes, we describe here a rational design of an artificial metalloenzyme for oxidations with the bacterial chaperonin GroEL, a nanocage for protein folding in nature, by supramolecular anchoring of catalytically active hemin in its hydrophobic central cavity. The promiscuity of the chaperonin cavity is an essential element of this design, which can mimic the hydrophobic binding pocket in natural metalloenzymes to accept cofactor and substrate without requiring specific ligand-protein interactions...
July 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28691708/an-exported-protein-interacting-complex-involved-in-the-trafficking-of-virulence-determinants-in-plasmodium-infected-erythrocytes
#7
Steven Batinovic, Emma McHugh, Scott A Chisholm, Kathryn Matthews, Boiyin Liu, Laure Dumont, Sarah C Charnaud, Molly Parkyn Schneider, Paul R Gilson, Tania F de Koning-Ward, Matthew W A Dixon, Leann Tilley
The malaria parasite, Plasmodium falciparum, displays the P. falciparum erythrocyte membrane protein 1 (PfEMP1) on the surface of infected red blood cells (RBCs). We here examine the physical organization of PfEMP1 trafficking intermediates in infected RBCs and determine interacting partners using an epitope-tagged minimal construct (PfEMP1B). We show that parasitophorous vacuole (PV)-located PfEMP1B interacts with components of the PTEX (Plasmodium Translocon of EXported proteins) as well as a novel protein complex, EPIC (Exported Protein-Interacting Complex)...
July 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28667536/natural-monoclonal-antibody-to-oxidized-low-density-lipoprotein-and-aggregatibacter-actinomycetemcomitans
#8
Chunguang Wang, Sohvi Hörkkö
Natural antibodies are produced by B lymphocytes without exogenous antigenic exposure and are present at the time of birth. They usually bind to conserved epitopes on antigens of different chemical compositions. We cloned and characterized a natural mouse monoclonal IgM antibody (Aa_Mab) by selecting the binding to malondialdehyde acetaldehyde (MAA) adducts on low-density lipoprotein (LDL). The data showed that the Aa_Mab cross-reacted with Aggregatibacter actinomycetemcomitans (Aa) bacteria, an important oral pathogen in periodontitis associated with atherosclerosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28665408/groel-actively-stimulates-folding-of-the-endogenous-substrate-protein-pepq
#9
Jeremy Weaver, Mengqiu Jiang, Andrew Roth, Jason Puchalla, Junjie Zhang, Hays S Rye
Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution...
June 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28628249/defining-a-temporal-order-of-genetic-requirements-for-development-of-mycobacterial-biofilms
#10
Yong Yang, Joseph Thomas, Yunlong Li, Catherine Vilchèze, Keith M Derbyshire, William R Jacobs, Anil K Ojha
Most mycobacterial species spontaneously form biofilms, inducing unique growth physiologies and reducing drug sensitivity. Biofilm growth progresses through three genetically programmed stages: substratum attachment, intercellular aggregation and architecture maturation. Growth of Mycobacterium smegmatis biofilms requires multiple factors including a chaperonin (GroEL1) and a nucleoid-associated protein (Lsr2), although how their activities are linked remains unclear. Here it is shown that Lsr2 participates in intercellular aggregation, but substratum attachment of Lsr2 mutants is unaffected, thereby genetically distinguishing these developmental stages...
June 19, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28623285/structure-of-the-human-tric-cct-subunit-5-associated-with-hereditary-sensory-neuropathy
#11
Jose H Pereira, Ryan P McAndrew, Oksana A Sergeeva, Corie Y Ralston, Jonathan A King, Paul D Adams
The human chaperonin TRiC consists of eight non-identical subunits, and its protein-folding activity is critical for cellular health. Misfolded proteins are associated with many human diseases, such as amyloid diseases, cancer, and neuropathies, making TRiC a potential therapeutic target. A detailed structural understanding of its ATP-dependent folding mechanism and substrate recognition is therefore of great importance. Of particular health-related interest is the mutation Histidine 147 to Arginine (H147R) in human TRiC subunit 5 (CCT5), which has been associated with hereditary sensory neuropathy...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28600765/detection-and-typing-of-candidatus-phytoplasma-spp-in-host-dna-extracts-using-oligonucleotide-coupled-fluorescent-microspheres
#12
Edel Pérez-López, Christine Hammond, Chrystel Olivier, Tim J Dumonceaux
The use of oligonucleotide-coupled fluorescent microspheres is a rapid, sequencing-independent, and reliable way to diagnose bacterial diseases. Previously described applications of oligonucleotide-coupled fluorescent microspheres for the detection and identification of bacteria in human clinical samples have been successfully adapted to detect and differentiate "Ca. Phytoplasma" species using as a target the chaperonin 60-encoding gene. In this chapter, we describe in detail the design and validation of oligonucleotide capture probes, and their application in the assay aiming to differentiate phytoplasma strains infecting Brassica napus and Camelina sativa plants grown in the same geographic location at the same time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28597961/non-housekeeping-non-essential-groel-chaperonin-has-acquired-novel-structure-and-function-beneficial-under-stress-in-cyanobacteria
#13
REVIEW
Hitoshi Nakamoto, Kouji Kojima
GroELs which are prokaryotic members of the chaperonin/Hsp60 family are molecular chaperones of which Escherichia coli GroEL is a model for subsequent research. The majority of bacterial species including E. coli and Bacillus subtilis have only one essential groEL gene that forms an operon with the co-chaperone groES gene.
June 9, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28594255/the-human-mitochondrial-hsp60-in-the-apo-conformation-forms-a-stable-tetradecameric-complex
#14
Adrian S Enriquez, Humberto M Rojo, Jay M Bhatt, Sudheer K Molugu, Zacariah L Hildenbrand, Ricardo A Bernal
The human mitochondrial chaperonin is a macromolecular machine that catalyzes the proper folding of mitochondrial proteins and is of vital importance to all cells. This chaperonin is composed of 2 distinct proteins, Hsp60 and Hsp10, that assemble into large oligomeric complexes that mediate the folding of non-native polypeptides in an ATP dependent manner. Here, we report the bacterial expression and purification of fully assembled human Hsp60 and Hsp10 recombinant proteins and that Hsp60 forms a stable tetradecameric double-ring conformation in the absence of co-chaperonin and nucleotide...
June 8, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28586052/a-novel-approach-to-select-differential-pathways-associated-with-hypertrophic-cardiomyopathy-based-on-gene-co%C3%A2-expression-analysis
#15
Xiao-Min Chen, Ming-Jun Feng, Cai-Jie Shen, Bin He, Xian-Feng Du, Yi-Bo Yu, Jing Liu, Hui-Min Chu
The present study was designed to develop a novel method for identifying significant pathways associated with human hypertrophic cardiomyopathy (HCM), based on gene co‑expression analysis. The microarray dataset associated with HCM (E‑GEOD‑36961) was obtained from the European Molecular Biology Laboratory‑European Bioinformatics Institute database. Informative pathways were selected based on the Reactome pathway database and screening treatments. An empirical Bayes method was utilized to construct co‑expression networks for informative pathways, and a weight value was assigned to each pathway...
July 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28583821/cloning-and-characterization-of-thermostable-groel-groes-homologues-from-geobacillus-thermopakistaniensis-and-their-applications-in-protein-folding
#16
Raza Ashraf, Majida Atta Muhammad, Naeem Rashid, Muhammad Akhtar
The chaperonin genes encoding GroELGt (ESU72018) and GroESGt (ESU72017), homologues of bacterial GroEL and GroES, from Geobacillus thermopakistaniensis were cloned and expressed in Escherichia coli. The purified gene products possessed the ATPase activity similar to other bacterial and eukaryal counterparts. Recombinant GroELGt and GroESGt were able to refold the denatured insoluble aggregates of α-amylase from Bacillus licheniformis into soluble and active form. Furthermore, GroELGt and GroESGt successfully enhanced the thermostability of porcine heart malate dehydrogenase...
June 3, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28572528/apex2-enhanced-electron-microscopy-distinguishes-sigma-1-receptor-localization-in-the-nucleoplasmic-reticulum
#17
Timur A Mavlyutov, Huan Yang, Miles L Epstein, Arnold E Ruoho, Jay Yang, Lian-Wang Guo
The sigma-1 receptor (Sig1R) is an endoplasmic reticulum chaperonin that is attracting tremendous interest as a potential anti-neurodegenerative target. While this membrane protein is known to reside in the inner nuclear envelope (NE) and influences transcription, apparent Sig1R presence in the nucleoplasm is often observed, seemingly contradicting its NE localization. We addressed this confounding issue by applying an antibody-free approach of electron microscopy (EM) to define Sig1R nuclear localization. We expressed APEX2 peroxidase fused to Sig1R-GFP in a Sig1R-null NSC34 neuronal cell line generated with CRISPR-Cas9...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28570583/metabolomic-and-proteomic-investigations-of-impacts-of-titanium-dioxide-nanoparticles-on-escherichia-coli
#18
Mariane Planchon, Thibaut Léger, Olivier Spalla, Gaspard Huber, Roselyne Ferrari
In a previous study, it was demonstrated that the toxic impact of titanium dioxide nanoparticles on Escherichia coli starts at 10 ppm and is closely related to the presence of little aggregates. It was also assumed that only a part of the bacterial population is able to adapt to this stress and attempts to survive. Proteomic analyses, supported by results from metabolomics, reveal that exposure of E. coli to nano-TiO2 induces two main effects on bacterial metabolism: firstly, the up-regulation of proteins and the increase of metabolites related to energy and growth metabolism; secondly, the down-regulation of other proteins resulting in an increase of metabolites, particularly amino acids...
2017: PloS One
https://www.readbyqxmd.com/read/28551403/chaperone-like-activity-of-synthetic-polyanions-can-be-higher-than-the-activity-of-natural-chaperones-at-elevated-temperature
#19
Pavel I Semenyuk, Lidia P Kurochkina, Nikolai B Gusev, Vladimir A Izumrudov, Vladimir I Muronetz
Polyelectrolytes are a prospective tool for protection of proteins against aggregation. We compared synthetic polyanion, poly(styrene sulfonate), and natural chaperones of different types, namely, GroEL-like chaperonin from Pseudomonas aeruginosa phage EL and human small heat shock protein HspB5 (αB-crystallin), in their ability to prevent aggregation of client proteins. At 45 °C, all three agents efficiently suppressed thermal aggregation of phage endolysin. At higher temperatures, HspB5 and poly(styrene sulfonate) also inhibited endolysin aggregation, though polyanion became less efficient than HspB5 at 55 °C and 60 °C...
May 24, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28534230/trueperella-pyogenes-isolated-from-a-brain-abscess-of-an-adult-roebuck-capreolus-capreolus
#20
Jörn-Peter Wickhorst, Abdulwahed Ahmed Hassan, Omar Hashim Sheet, Tobias Eisenberg, Osama Sammra, Mazen Alssahen, Christoph Lämmler, Ellen Prenger-Berninghoff, Michael Zschöck, Markus Timke, Amir Abdulmawjood
The present study was designed to characterize phenotypically and genotypically a Trueperella pyogenes strain isolated from a brain abscess of an adult roebuck (Capreolus capreolus). The species identity could be confirmed by phenotypical investigations, by MALDI-TOF MS analysis, and by sequencing the 16S ribosomal RNA (rRNA) gene, the 16S-23S rRNA intergenic spacer region (ISR); by sequencing the target genes rpoB, gap, and tuf; and by detection of T. pyogenes chaperonin-encoding gene cpn60 with a previously developed loop-mediated isothermal amplification (LAMP) assay...
May 23, 2017: Folia Microbiologica
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