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https://www.readbyqxmd.com/read/29160034/free-living-chemoautotrophic-and-particle-attached-heterotrophic-prokaryotes-dominate-microbial-assemblages-along-a-pelagic-redox-gradient
#1
Elizabeth A Suter, Maria Pachiadaki, Gordon T Taylor, Yrene Astor, Virginia P Edgcomb
Using the anoxic Cariaco Basin as a natural laboratory, particle association of bacterial and archaeal taxa was assessed by iTag sequencing and qPCR gene assays of samples spanning an oxic-anoxic-euxinic gradient. Ten to twelve percent of all bacterial and archaeal cells were found in the particle-associated (PA) fraction, operationally defined as prokaryotes captured on 2.7µm membranes. Both redox condition and size fraction segregated bacterial taxa. Archaeal taxa varied according to redox conditions, but were similar between size fractions...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29155472/experimental-reconstruction-of-double-strand-break-repair-mediated-plastid-dna-insertion-into-the-tobacco-nucleus
#2
Dong Wang, Jinbao Gu, Rakesh David, Zhen Wang, Songtao Yang, Iain R Searle, Jian-Kang Zhu, Jeremy N Timmis
The mitochondria and plastids of eukaryotic cells evolved from endosymbiotic prokaryotes. DNA from the endosymbionts has bombarded nuclei since the ancestral prokaryotes were engulfed by a precursor of the nucleated eukaryotic host. An experimental confirmation regarding the molecular mechanisms responsible for organelle DNA incorporation into nuclei has not been performed until the present analysis. Here we introduced double-strand DNA breaks into the nuclear genome of tobacco through inducible expression of I-SceI, and showed experimentally that tobacco chloroplast DNAs insert into nuclear genomes through double-strand DNA break repair...
November 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29152201/the-natural-selection-of-metabolism-and-mass-selects-lifeforms-from-viruses-to-multicellular-animals
#3
Lars Witting
I show that the natural selection of metabolism and mass can select for the major life-history and allometric transitions that define lifeforms from viruses, over prokaryotes and larger unicells, to multicellular animals. The proposed selection is driven by a mass-specific metabolism that is selected as the pace of the resource handling that generates net energy for self-replication. An initial selection of mass is given by a dependence of mass-specific metabolism on mass in replicators that are close to a lower size limit...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29151221/quantitative-determination-of-interacting-protein-surfaces-in-prokaryotes-and-eukaryotes-by-using-in-cell-nmr-spectroscopy
#4
David S Burz, Christopher M DeMott, Asma Aldousary, Stephen Dansereau, Alexander Shekhtman
This paper describes three protocols for identifying interacting surfaces on (15)N-labeled target proteins of known structure by using in-cell NMR spectroscopy. The first protocol describes how to identify protein quinary structure interaction surfaces in prokaryotes by using cross-relaxation-induced polarization transfer, CRIPT, based in-cell NMR. The second protocol describes how to introduce labeled protein into eukaryotic (HeLa) cells via electroporation for CRIPT-based in-cell studies. The third protocol describes how to quantitatively map protein interacting surfaces by utilizing singular value decomposition, SVD, analysis of STructural INTeractions by in-cell NMR, STINT-NMR, data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29150981/systematic-proteomic-analysis-of-protein-methylation-in-prokaryotes-and-eukaryotes-revealed-distinct-substrate-specificity
#5
Min Zhang, Jun-Yu Xu, Hao Hu, Bang-Ce Ye, Minjia Tan
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, was largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29148923/ames-and-random-amplified-polymorphic-dna-tests-for-the-validation-of-the-mutagenic-and-or-genotoxic-potential-of-the-drinking-water-disinfection-by-products-chloroform-and-bromoform
#6
Messaouda Khallef, Süleyman Cenkci, Dilek Akyil, Arzu Özkara, Muhsin Konuk, Djamel Eddine Benouareth
Chloroform and Bromoform are two abundant trihalomethanes found in Algerian drinking water. The investigation of the mutagenic hazard of these disinfection by-products was studied by Ames test as prokaryotic bioassay to show their mutagenic effects. For this, Salmonella typhimurium TA98 and TA100 strains were employed. Both chloroform and bromoform showed a direct mutagenic effect since the number of revertant colonies gradually increase in dose-dependent manner with all concentrations tested with the two bacterial strains and these were both in the absence and presence of S9 metabolic activation...
November 17, 2017: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/29140245/bacterial-fumarase-and-l-malic-acid-are-evolutionary-ancient-components-of-the-dna-damage-response
#7
Esti Singer, Yardena Bh Silas, Sigal Ben-Yehuda, Ophry Pines
Fumarase is distributed between two compartments of the eukaryotic cell. The enzyme catalyses the reversible conversion of fumaric to L-malic acid in mitochondria as part of the tricarboxylic acid (TCA) cycle, and in the cytosol/nucleus as part of the DNA damage response (DDR). Here we show that fumarase of the model prokaryote Bacillus subtilis (Fum-bc) is induced upon DNA damage, co-localized with the bacterial DNA and is required for the DDR. Fum-bc can substitute for both eukaryotic functions in yeast. Furthermore, we found that the fumarase dependent intracellular signaling of the B...
November 15, 2017: ELife
https://www.readbyqxmd.com/read/29133784/gyri-like-proteins-catalyze-cyclopropanoid-hydrolysis-to-confer-cellular-protection
#8
Hua Yuan, Jinru Zhang, Yujuan Cai, Sheng Wu, Kui Yang, H C Stephen Chan, Wei Huang, Wen-Bing Jin, Yan Li, Yue Yin, Yasuhiro Igarashi, Shuguang Yuan, Jiahai Zhou, Gong-Li Tang
GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29131838/expanded-repertoire-of-kinetoplast-associated-proteins-and-unique-mitochondrial-dna-arrangement-of-symbiont-bearing-trypanosomatids
#9
Silvana Sant Anna de Souza, Carolina Moura Catta-Preta, João Marcelo P Alves, Danielle P Cavalcanti, Marta M G Teixeira, Erney P Camargo, Wanderley De Souza, Rosane Silva, Maria Cristina M Motta
In trypanosomatids, the kinetoplast is the portion of the single mitochondrion that is connected to the basal body and contains the kDNA, a network composed by circular and interlocked DNA. The kDNA packing is conducted by Kinetoplast Associated Proteins (KAPs), which are similar to eukaryotic histone H1. In symbiont-harboring trypanosomatids (SHTs) such as Angomonas deanei and Strigomonas culicis, a ß-proteobacterium co-evolves with the host in a mutualistic relationship. The prokaryote confers nutritional benefits to the host and affects its cell structure...
2017: PloS One
https://www.readbyqxmd.com/read/29130151/viral-vectors-engineered-cells-and-the-crispr-revolution
#10
James E DiCarlo, Anurag Deeconda, Stephen H Tsang
Over the past few decades the ability to edit human cells has revolutionized modern biology and medicine. With advances in genome editing methodologies, gene delivery and cell-based therapeutics targeted at treatment of genetic disease have become a reality that will become more and more essential in clinical practice. Modifying specific mutations in eukaryotic cells using CRISPR-Cas systems derived from prokaryotic immune systems has allowed for precision in correcting various disease mutations. Furthermore, delivery of genetic payloads by employing viral tropism has become a crucial and effective mechanism for delivering genes and gene editing systems into cells...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29129605/evolution-and-adaptation-of-single-pass-transmembrane-proteins
#11
Irina D Pogozheva, Andrei L Lomize
A comparative analysis of 6,039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication...
November 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29127003/recombinant-alpha-fetoprotein-receptor-binding-domain-co-expression-with-polyglutamate-tags-facilitates-in-vivo-folding-in-e-coli
#12
Murad Mollaev, Neonila Gorokhovets, Elena Nikolskaya, Maria Faustova, Arthur Zabolotsky, Maria Sokol, Oksana Tereshenko, Olga Zhunina, Vitaliy Shvets, Evgeniy Severin, Nikita Yabbarov
A wide range of methods are known to increase the prokaryotic intracellular recombinant proteins solubility, for instance, growth at low temperature, supplementation of culture media with "chemical chaperones" (proline, glycine-betaine, and trehalose), co-expression with chaperones or highly soluble fusion partners. As an alternative, we have introduced the polyglutamate tag, which, as it has been shown, increased the protein solubility and facilitated folding. In this study we evaluated the minimal quantity of high density negatively charged EEEEVE amino acid repeats (pGlu) necessary to switch the recombinant receptor-binding domain of human alpha-fetoprotein (rbdAFP) expression almost entirely from the inclusion bodies to the soluble cytoplasmic fraction in E...
November 7, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/29124868/obligate-sugar-oxidation-in-mesotoga-spp-phylum-thermotogae-in-the-presence-of-either-elemental-sulfur-or-hydrogenotrophic-sulfate-reducers-as-electron-acceptor
#13
Khaled Fadhlaoui, Wagdi Ben Hania, Fabrice Armougom, Manon Bartoli, Marie-Laure Fardeau, Gaël Erauso, Gaël Brasseur, Corinne Aubert, Moktar Hamdi, Céline Brochier-Armanet, Alain Dolla, Bernard Ollivier
Mesotoga prima strain PhosAc3 is a mesophilic representative of the phylum Thermotogae comprising only fermentative bacteria so far. We show that while unable to ferment glucose, this bacterium is able to couple its oxidation to reduction of elemental sulfur. We demonstrate furthermore that M. prima strain PhosAc3 as well as M. prima strain MesG1 and M. infera are able to grow in syntrophic association with sulfate-reducing bacteria (SRB) acting as hydrogen scavengers through interspecies hydrogen transfer...
November 10, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29123677/in-vivo-analysis-of-the-escherichia-coli-ultrastructure-by-small-angle-scattering
#14
Enrico F Semeraro, Juliette M Devos, Lionel Porcar, V Trevor Forsyth, Theyencheri Narayanan
The flagellated Gram-negative bacterium Escherichia coli is one of the most studied microorganisms. Despite extensive studies as a model prokaryotic cell, the ultrastructure of the cell envelope at the nanometre scale has not been fully elucidated. Here, a detailed structural analysis of the bacterium using a combination of small-angle X-ray and neutron scattering (SAXS and SANS, respectively) and ultra-SAXS (USAXS) methods is presented. A multiscale structural model has been derived by incorporating well established concepts in soft-matter science such as a core-shell colloid for the cell body, a multilayer membrane for the cell wall and self-avoiding polymer chains for the flagella...
November 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/29123225/archaea-and-the-origin-of-eukaryotes
#15
REVIEW
Laura Eme, Anja Spang, Jonathan Lombard, Courtney W Stairs, Thijs J G Ettema
Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features...
November 10, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29119849/graphene-oxide-significantly-inhibits-cell-growth-at-sublethal-concentrations-by-causing-extracellular-iron-deficiency
#16
Qilin Yu, Bing Zhang, Jianrong Li, Tingting Du, Xiao Yi, Mingchun Li, Wei Chen, Pedro J J Alvarez
Graphene oxide (GO)-based materials are increasingly being used in medical materials and consumer products. However, their sublethal effects on biological systems are poorly understood. Here, we report that GO (at 10 to 160 mg/L) induced significant inhibitory effects on the growth of different unicellular organisms, including eukaryotes (i.e. Saccharomyces cerevisiae, Candida albicans, and Komagataella pastoris) and prokaryotes (Pseudomonas fluorescens). Growth inhibition could not be explained by commonly reported cytotoxicity mechanisms such as plasma membrane damage or oxidative stress...
November 9, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/29119102/the-transcriptional-network-structure-of-a-myeloid-cell-a-computational-approach
#17
Jesús Espinal-Enríquez, Daniel González-Terán, Enrique Hernández-Lemus
Understanding the general principles underlying genetic regulation in eukaryotes is an incomplete and challenging endeavor. The lack of experimental information regarding the regulation of the whole set of transcription factors and their targets in different cell types is one of the main reasons to this incompleteness. So far, there is a small set of curated known interactions between transcription factors and their downstream genes. Here, we built a transcription factor network for human monocytic THP-1 myeloid cells based on the experimentally curated FANTOM4 database where nodes are genes and the experimental interactions correspond to links...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29119038/visualization-of-phage-dna-degradation-by-a-type-i-crispr-cas-system-at-the-single-cell-level
#18
Jingwen Guan, Xu Shi, Roberto Burgos, Lanying Zeng
Background: The CRISPR-Cas system is a widespread prokaryotic defense system which targets and cleaves invasive nucleic acids, such as plasmids or viruses. So far, a great number of studies have focused on the components and mechanisms of this system, however, a direct visualization of CRISPR-Cas degrading invading DNA in real-time has not yet been studied at the single-cell level. Methods: In this study, we fluorescently label phage lambda DNA in vivo, and track the labeled DNA over time to characterize DNA degradation at the single-cell level...
March 2017: Quantitative Biology
https://www.readbyqxmd.com/read/29117437/measuring-%C3%AE-galactosidase-activity-in-gram-positive-bacteria-using-a-whole-cell-assay-with-mug-as-a-fluorescent-reporter
#19
Norman H L Chiu, Amanda L Watson
The use of β-galactosidase enzyme as a biomarker has the potential to determine activity levels of the microbiome of a variety of organisms due to its common presence in both eukaryotes and prokaryotes. Completing the assay in a whole-cell format facilitates the monitoring of β-galactosidase activity in its actual cellular environment. This unit describes an optimized fluorescent assay for β-galactosidase that has enough sensitivity to detect the enzymatic activity despite the thick gram-positive bacterial cellular membrane...
November 8, 2017: Current Protocols in Toxicology
https://www.readbyqxmd.com/read/29114403/transcriptomic-analysis-of-aerobic-respiratory-and-anaerobic-photosynthetic-states-in-rhodobacter-capsulatus-and-their-modulation-by-global-redox-regulators-rega-fnrl-and-crtj
#20
Joseph E Kumka, Heidi Schindel, Mingxu Fang, Sebastien Zappa, Carl E Bauer
Anoxygenicphotosynthetic prokaryotes have simplified photosystems that represent ancient lineages that predate the more complex oxygen evolving photosystems present in cyanobacteria and chloroplasts. These organisms thrive under illuminated anaerobic photosynthetic conditions, but also have the ability to grow under dark aerobic respiratory conditions. This study provides a detailed snapshot of transcription ground states of both dark aerobic and anaerobic photosynthetic growth modes in the purple photosynthetic bacterium Rhodobactercapsulatus...
September 2017: Microbial Genomics
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