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lipid modification and sequencing

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https://www.readbyqxmd.com/read/29764287/function-of-a-membrane-embedded-domain-evolutionarily-multiplied-in-the-gpi-lipid-anchor-pathway-proteins-pig-b-pig-m-pig-u-pig-w-pig-v-and-pig-z
#1
Birgit Eisenhaber, Swati Sinha, Wing-Cheong Wong, Frank Eisenhaber
Distant homology relationships among proteins with many transmembrane regions (TMs) are difficult to detect as they are clouded by the TMs' hydrophobic compositional bias and mutational divergence in connecting loops. In the case of several GPI lipid anchor biosynthesis pathway components, the hidden evolutionary signal can be revealed with dissectHMMER, a sequence similarity search tool focusing on fold-critical, high complexity sequence segments. We find that a sequence module with 10 TMs in PIG-W, described as acyl transferase, is homologous to PIG-U, a transamidase subunit without characterized molecular function, and to mannosyltransferases PIG-B, PIG-M, PIG-V and PIG-Z...
May 15, 2018: Cell Cycle
https://www.readbyqxmd.com/read/29755416/complete-genomic-analysis-of-a-salmonella-enterica-serovar-typhimurium-isolate-cultured-from-ready-to-eat-pork-in-china-carrying-one-large-plasmid-containing-mcr-1
#2
Wei Wang, Zulqarnain Baloch, Mingyuan Zou, Yinping Dong, Zixin Peng, Yujie Hu, Jin Xu, Nafeesa Yasmeen, Fengqin Li, Séamus Fanning
One mcr-1 -carrying ST34-type Salmonella Typhimurium WW012 was cultured from 3,200 ready-to-eat (RTE) pork samples in 2014 in China. Broth dilution method was applied to obtain the antimicrobial susceptibility of Salmonella Typhimurium WW012. Broth matting assays were carried out to detect transferability of this phenotype and whole-genome sequencing was performed to analyze its genomic characteristic. Thirty out of 3,200 RTE samples were positive for Salmonella and the three most frequent serotypes were identified as S ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29695963/the-effects-of-ppar-stimulation-on-cardiac-metabolic-pathways-in-barth-syndrome-mice
#3
Caitlin Schafer, Vicky Moore, Nupur Dasgupta, Sabzali Javadov, Jeanne F James, Alexander I Glukhov, Arnold W Strauss, Zaza Khuchua
Aim: Tafazzin knockdown (TazKD) in mice is widely used to create an experimental model of Barth syndrome (BTHS) that exhibits dilated cardiomyopathy and impaired exercise capacity. Peroxisome proliferator-activated receptors (PPARs) are a group of nuclear receptor proteins that play essential roles as transcription factors in the regulation of carbohydrate, lipid, and protein metabolism. We hypothesized that the activation of PPAR signaling with PPAR agonist bezafibrate (BF) may ameliorate impaired cardiac and skeletal muscle function in TazKD mice...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29588502/extensive-molecular-tinkering-in-the-evolution-of-the-membrane-attachment-mode-of-the-rheb-gtpase
#4
Kristína Záhonová, Romana Petrželková, Matus Valach, Euki Yazaki, Denis V Tikhonenkov, Anzhelika Butenko, Jan Janouškovec, Štěpánka Hrdá, Vladimír Klimeš, Gertraud Burger, Yuji Inagaki, Patrick J Keeling, Vladimír Hampl, Pavel Flegontov, Vyacheslav Yurchenko, Marek Eliáš
Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifications include: (1) accretion to the N-terminus of two different phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the first proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed flagellate SRT308; (2) acquisition of lipidic modifications of the N-terminal region, namely myristoylation and/or S-palmitoylation in seven different protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa...
March 27, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29556049/genetically-encoded-lipid-polypeptide-hybrid-biomaterials-that-exhibit-temperature-triggered-hierarchical-self-assembly
#5
Davoud Mozhdehi, Kelli M Luginbuhl, Joseph R Simon, Michael Dzuricky, Rüdiger Berger, H Samet Varol, Fred C Huang, Kristen L Buehne, Nicholas R Mayne, Isaac Weitzhandler, Mischa Bonn, Sapun H Parekh, Ashutosh Chilkoti
Post-translational modification of proteins is a strategy widely used in biological systems. It expands the diversity of the proteome and allows for tailoring of both the function and localization of proteins within cells as well as the material properties of structural proteins and matrices. Despite their ubiquity in biology, with a few exceptions, the potential of post-translational modifications in biomaterials synthesis has remained largely untapped. As a proof of concept to demonstrate the feasibility of creating a genetically encoded biohybrid material through post-translational modification, we report here the generation of a family of three stimulus-responsive hybrid materials-fatty-acid-modified elastin-like polypeptides-using a one-pot recombinant expression and post-translational lipidation methodology...
March 19, 2018: Nature Chemistry
https://www.readbyqxmd.com/read/29524395/headgroup-hydroxylation-by-olse-occurs-at-the-c4-position-of-ornithine-lipid-and-is-widespread-in-proteobacteria-and-bacteroidetes
#6
Georg Hölzl, Christian Sohlenkamp, Miguel Angel Vences-Guzmán, Nicolas Gisch
Amino acid-containing acyloxyacyl lipids are composed of a 3-hydroxy fatty acid amide-bound to the α-amino group of an amino acid. A second fatty acid is ester-linked to the 3-hydroxy group of the first fatty acid. Most commonly, ornithine is the headgroup of these lipids, but glycine, serineglycine, glutamine and lysine have also been described in bacteria. Ornithine lipids (OL) can be synthesized by about 50% of the sequenced bacterial species, and several covalent modifications of its basic structure have been described...
March 7, 2018: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/29521624/functional-genomics-of-lipid-metabolism-in-the-oleaginous-yeast-rhodosporidium-toruloides
#7
Samuel T Coradetti, Dominic Pinel, Gina M Geiselman, Masakazu Ito, Stephen J Mondo, Morgann C Reilly, Ya-Fang Cheng, Stefan Bauer, Igor V Grigoriev, John M Gladden, Blake A Simmons, Rachel B Brem, Adam P Arkin, Jeffrey M Skerker
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides ) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains...
March 9, 2018: ELife
https://www.readbyqxmd.com/read/29487348/mrna-m-6-a-plays-opposite-role-in-regulating-ucp2-and-pnpla2-protein-expression-in-adipocytes
#8
Xinxia Wang, Baofa Sun, Qin Jiang, Ruifan Wu, Min Cai, Yongxi Yao, Qing Liu, Hailing Shi, Jie Feng, Yizhen Wang
BACKGROUND/OBJECTIVE: N6 -methyladenosine (m6 A) modification of mRNA plays an important role in regulating adipogenesis. However, its underlying mechanism remains largely unknown. SUBJECTS/METHODS: Using Jinhua and Landrace pigs as fat and lean models, we presented a comprehensive transcriptome-wide m6 A profiling in adipose tissues from these two pig breeds. Two differentially methylated genes were selected to explore the mechanisms of m6 A-mediated regulation of gene function...
February 27, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29422865/dietary-safety-assessment-of-flk1-transgenic-fish
#9
Yalan Wei, Ling Huang, Jinghui Cao, Chenghui Wang, Jizhou Yan
Genetic engineering, also called genetic modification, is facing with growing demands of aquaculture and aquatic products. Although various genetically modified (GM) aquatics have been generated, it is important to evaluate biosafety of GM organisms on the human health before entering into our food chain. For this purpose, we establish a zebrafish wild adult feeding Flk1-transgenic larvae model to examine the predatory fish's histology in multiple tissues, and the global gene expression profile in the liver...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29376493/placental-exosomes-during-gestation-liquid-biopsies-carrying-signals-for-the-regulation-of-human-parturition
#10
Carlos Salomon, Zarin Nuzhat, Christopher L Dixon, Ramkumar Menon
Parturition is defined as the action or process of giving birth to offspring. Normal term human parturition ensues following the maturation of fetal organ systems typically between 37 and 40 weeks of gestation. Our conventional understanding of how parturition initiation is signaled revolves around feto-maternal immune and endocrine changes occurring in the intrauterine cavity. These changes in turn correlate with the sequence of fetal growth and development. These important physiological changes also result in homeostatic imbalances which result in heightened inflammatory signaling...
January 25, 2018: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/29320326/mediastinal-and-pleural-mr-imaging-practical-approach-for-daily-practice
#11
Constantine A Raptis, Sebastian R McWilliams, Kristy L Ratkowski, Jordi Broncano, Daniel B Green, Sanjeev Bhalla
Radiologists in any practice setting should be prepared to use thoracic magnetic resonance (MR) imaging for noncardiac and nonangiographic applications. This begins with understanding the sequence building blocks that can be used to design effective thoracic MR imaging protocols. In most instances, the sequences used in thoracic MR imaging are adapted from protocols used elsewhere in the body. Some modifications, including the addition of electrocardiographic gating or respiratory triggering, may be necessary for certain applications...
January 2018: Radiographics: a Review Publication of the Radiological Society of North America, Inc
https://www.readbyqxmd.com/read/29288722/comparative-analysis-of-phosphoethanolamine-transferases-involved-in-polymyxin-resistance-across-10-clinically-relevant-gram-negative-bacteria
#12
Jiayuan Huang, Yan Zhu, Mei-Ling Han, Mengyao Li, Jiangning Song, Tony Velkov, Chen Li, Jian Li
The rapid emergence of Gram-negative 'superbugs' has become a significant threat to human health globally, and polymyxins have become a last-line therapy for these very problematic pathogens. Polymyxins exhibit their antibacterial killing by initial interaction with lipid A in Gram-negative bacteria. Polymyxin resistance can be mediated by phosphoethanolamine (PEA) modification of lipid A, which abolishes the initial electrostatic interaction with polymyxins. Both chromosome-encoded (e.g. EptA, EptB and EptC) and plasmid-encoded (e...
April 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29235492/proteome-wide-analysis-of-lysine-2-hydroxyisobutyrylation-in-developing-rice-oryza-sativa-seeds
#13
Xiaoxi Meng, Shihai Xing, Loida M Perez, Xiaojun Peng, Qingyong Zhao, Edilberto D Redoña, Cailin Wang, Zhaohua Peng
Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lysine 2-hydroxyisobutyrylome dataset in plants...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29226611/enhancing-the-stability-and-immunomodulatory-activity-of-liposomal-spherical-nucleic-acids-through-lipid-tail-dna-modifications
#14
Brian Meckes, Resham J Banga, SonBinh T Nguyen, Chad A Mirkin
Liposomal spherical nucleic acids (LSNAs) are an attractive therapeutic platform for gene regulation and immunomodulation due to their biocompatibility, chemically tunable structures, and ability to enter cells rapidly without the need for ancillary transfection agents. Such structures consist of small (<100 nm) liposomal cores functionalized with a dense, highly oriented nucleic acid shell, both of which are key components in facilitating their biological activity. Here, the properties of LSNAs synthesized using conventional methods, anchoring cholesterol terminated oligonucleotides into a liposomal core, are compared to LSNAs made by directly modifying the surface of a liposomal core containing azide-functionalized lipids with dibenzocyclooctyl-terminated oligonucleotides...
February 2018: Small
https://www.readbyqxmd.com/read/29208119/comparative-analysis-of-the-burkholderia-cenocepacia-k56-2-essential-genome-reveals-cell-envelope-functions-that-are-uniquely-required-for-survival-in-species-of-the-genus-burkholderia
#15
April S Gislason, Keith Turner, Mike Domaratzki, Silvia T Cardona
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations...
November 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29180119/cyclopropane-fatty-acid-synthesis-affects-cell-shape-and-acid-resistance-in-leishmania-mexicana
#16
Wei Xu, Sumit Mukherjee, Yu Ning, Fong-Fu Hsu, Kai Zhang
Cyclopropane fatty acid synthase (CFAS) catalyzes the transfer of a methylene group from S-adenosyl methionine to an unsaturated fatty acid, generating a cyclopropane fatty acid (CFA). The gene encoding CFAS is present in many bacteria and several Leishmania spp. including Leishmania mexicana, Leishmania infantum and Leishmania braziliensis. In this study, we characterised the CFAS-null and -overexpression mutants in L. mexicana, the causative agent for cutaneous leishmaniasis in Mexico and central America...
March 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29140585/timap-the-versatile-protein-phosphatase-1-regulator-in-endothelial-cells
#17
REVIEW
Anita Boratkó, Csilla Csortos
Transforming growth factor (TGF)-β inhibited membrane associated protein, TIMAP, is the member of the myosin phosphatase targeting protein (MYPT) family of protein phosphatase 1 (PP1) regulatory subunits. The N-terminal part of TIMAP has a typical MYPT family structure with a sequence element called MyPhone (myosin phosphatase N-terminal element), a putative bipartite nuclear localization signal, a PP1 catalytic subunit binding motif, and five ankyrin repeats. The C-terminal half of TIMAP is intrinsically disordered, but ends with a functional CAAX box for lipid modification which allows localization of TIMAP at the plasma membrane...
November 15, 2017: IUBMB Life
https://www.readbyqxmd.com/read/29120602/porphyrin-assisted-docking-of-a-thermophage-portal-protein-into-lipid-bilayers-nanopore-engineering-and-characterization
#18
Benjamin Cressiot, Sandra J Greive, Wei Si, Tomas C Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw T Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A Antson, Meni Wanunu
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein...
December 26, 2017: ACS Nano
https://www.readbyqxmd.com/read/29042445/analysis-of-substrate-specificity-of-trypanosoma-brucei-oligosaccharyltransferases-osts-by-functional-expression-of-domain-swapped-chimeras-in-yeast
#19
Kristina Poljak, Jörg Breitling, Robert Gauss, George Rugarabamu, Mauro Pellanda, Markus Aebi
N -Linked protein glycosylation is an essential and highly conserved post-translational modification in eukaryotes. The transfer of a glycan from a lipid-linked oligosaccharide (LLO) donor to the asparagine residue of a nascent polypeptide chain is catalyzed by an oligosaccharyltransferase (OST) in the lumen of the endoplasmic reticulum (ER). Trypanosoma brucei encodes three paralogue single-protein OSTs called Tb STT3A, Tb STT3B, and Tb STT3C that can functionally complement the Saccharomyces cerevisiae OST, making it an ideal experimental system to study the fundamental properties of OST activity...
December 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29036931/mass-spectrometric-studies-of-apolipoprotein-proteoforms-and-their-role-in-lipid-metabolism-and-type-2-diabetes
#20
REVIEW
Dobrin Nedelkov
Apolipoproteins function as structural components of lipoprotein particles, cofactors for enzymes, and ligands for cell-surface receptors. Most of the apoliporoteins exhibit proteoforms, arising from single nucleotide polymorphisms (SNPs) and post-translational modifications such as glycosylation, oxidation, and sequence truncations. Reviewed here are recent studies correlating apolipoproteins proteoforms with the specific clinical measures of lipid metabolism and cardiometabolic risk. Targeted mass spectrometric immunoassays toward apolipoproteins A-I, A-II, and C-III were applied on large cross-sectional and longitudinal clinical cohorts...
October 15, 2017: Proteomes
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