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lipid modification and sequencing

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https://www.readbyqxmd.com/read/29042445/analysis-of-substrate-specificity-of-trypanosoma-brucei-osts-by-functional-expression-of-domain-swapped-chimeras-in-yeast
#1
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 TbSTT3A, TbSTT3B and TbSTT3C that can functionally complement the Saccharomyces cerevisiae OST, making it an ideal experimental system to study the fundamental properties of OST activity...
October 17, 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
#2
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
https://www.readbyqxmd.com/read/29020117/a-putative-vibrio-cholerae-two-component-system-controls-a-conserved-periplasmic-protein-in-response-to-the-antimicrobial-peptide-polymyxin-b
#3
Jyl S Matson, Jonathan Livny, Victor J DiRita
The epidemic pathogen Vibrio cholerae senses and responds to different external stresses it encounters in the aquatic environment and in the human host. One stress that V. cholerae encounters in the host is exposure to antimicrobial peptides on mucosal surfaces. We used massively parallel cDNA sequencing (RNA-Seq) to quantitatively identify the transcriptome of V. cholerae grown in the presence and absence of sub-lethal concentrations of the antimicrobial peptide polymyxin B. We evaluated the transcriptome of both wild type V...
2017: PloS One
https://www.readbyqxmd.com/read/28990612/controlling-g-quadruplex-formation-via-lipid-modification-of-oligonucleotide-sequences
#4
Brune Vialet, Arnaud Gissot, Romain Delzor, Philippe Barthélémy
G-quadruplexes (G4) represent attractive supramolecular scaffolds. In this communication, we show that the lipid modification of a G4 prone oligonucleotide sequence drastically increases the probability of forming tetramolecular parallel G4s with unprecedented conformational control over other unspecific oligomers or folds.
October 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28983469/population-genomic-insights-into-variation-in-prevotella-intermedia-and-prevotella-nigrescens-isolates-and-its-association-with-periodontal-disease
#5
Yifei Zhang, Min Zhen, Yalin Zhan, Yeqing Song, Qian Zhang, Jinfeng Wang
High-throughput sequencing has helped to reveal the close relationship between Prevotella and periodontal disease, but the roles of subspecies diversity and genomic variation within this genus in periodontal diseases still need to be investigated. We performed a comparative genome analysis of 48 Prevotella intermedia and Prevotella nigrescens isolates that from the same cohort of subjects to identify the main drivers of their pathogenicity and adaptation to different environments. The comparisons were done between two species and between disease and health based on pooled sequences...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28961916/structural-modification-of-lps-in-colistin-resistant-kpc-producing-klebsiella-pneumoniae
#6
Lisa M Leung, Vaughn S Cooper, David A Rasko, Qinglan Guo, Marissa P Pacey, Christi L McElheny, Roberta T Mettus, Sung Hwan Yoon, David R Goodlett, Robert K Ernst, Yohei Doi
Background: Colistin resistance in Klebsiella pneumoniae typically involves inactivation or mutations of chromosomal genes mgrB , pmrAB or phoPQ , but data regarding consequent modifications of LPS are limited. Objectives: To examine the sequences of chromosomal loci implicated in colistin resistance and the respective LPS-derived lipid A profiles using 11 pairs of colistin-susceptible and -resistant KPC-producing K. pneumoniae clinical strains. Methods: The strains were subjected to high-throughput sequencing with Illumina HiSeq...
August 18, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28953347/highly-potent-antibacterial-organometallic-peptide-conjugates
#7
Bauke Albada, Nils Metzler-Nolte
Resistance of pathogenic bacteria against currently marketed antibiotics is again increasing. To meet the societal need for effective cures, scientists are faced with the challenge of developing more potent but equally bacteria-specific drugs. Currently, most efforts are directed toward the modification of existing antibiotics, but ideally, compounds with a new mode of action are required. In this Account, we detail our findings in the area of novel metal-based antibiotics. Our strategy is based on the modification of simple antimicrobial peptides (AMPs) with organometallic agents, resulting in organometallic AMPs (OM-AMPs)...
October 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28939768/plasma-membrane-phosphatidylinositol-4-phosphate-and-4-5-bisphosphate-determine-the-distribution-and-function-of-k-ras4b-but-not-h-ras-proteins
#8
Gergö Gulyás, Glória Radvánszki, Rita Matuska, András Balla, László Hunyady, Tamas Balla, Péter Várnai
Plasma membrane (PM) localization of Ras proteins is crucial for transmitting signals upon mitogen stimulation. Posttranslational lipid modification of Ras proteins plays an important role in their recruitment to the PM. Electrostatic interactions between negatively charged PM phospholipids and basic amino acids found in K-Ras4B (K-Ras) but not in H-Ras are important for permanent K-Ras localization to the PM. Here, we investigated how acute depletion of negatively charged PM polyphosphoinositides (PPIns) from the PM alters the intracellular distribution and activity of K- and H-Ras proteins...
September 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28932871/crystal-structures-of-eukaryote-glycosyltransferases-reveal-biologically-relevant-enzyme-homooligomers
#9
REVIEW
Deborah Harrus, Sakari Kellokumpu, Tuomo Glumoff
Glycosyltransferases (GTases) transfer sugar moieties to proteins, lipids or existing glycan or polysaccharide molecules. GTases form an important group of enzymes in the Golgi, where the synthesis and modification of glycoproteins and glycolipids take place. Golgi GTases are almost invariably type II integral membrane proteins, with the C-terminal globular catalytic domain residing in the Golgi lumen. The enzymes themselves are divided into 103 families based on their sequence homology. There is an abundance of published crystal structures of GTase catalytic domains deposited in the Protein Data Bank (PDB)...
September 20, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28928222/single-subunit-oligosaccharyltransferases-of-trypanosoma-brucei-display-different-and-predictable-peptide-acceptor-specificities
#10
Anders A J Jinnelov, Liaqat Ali, Michele Tinti, Michael A J Ferguson
Trypanosoma brucei causes African trypanosomiasis and contains three full-length oligosaccharyltransferase (OST) genes; two of which, TbSTT3A and TbSTT3B, are expressed in the bloodstream form of the parasite. These OSTs have different peptide acceptor and lipid-linked oligosaccharide donor specificities and trypanosomes do not follow many of the canonical rules developed for other eukaryotic N-glycosylation pathways, raising questions as to the basic architecture and detailed function of trypanosome OSTs. Here, we show by blue-native gel electrophoresis and stable isotope labelling in cell culture proteomics that the TbSTT3A and TbSTT3B proteins associate with each other in large complexes that contain no other detectable protein subunits...
September 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28899409/alcohol-consumption-and-breast-tumor-gene-expression
#11
Jun Wang, Yujing J Heng, A Heather Eliassen, Rulla M Tamimi, Aditi Hazra, Vincent J Carey, Christine B Ambrosone, Victor P de Andrade, Adam Brufsky, Fergus J Couch, Tari A King, Francesmary Modugno, Celine M Vachon, David J Hunter, Andrew H Beck, Susan E Hankinson
BACKGROUND: Alcohol consumption is an established risk factor for breast cancer and the association generally appears stronger among estrogen receptor (ER)-positive tumors. However, the biological mechanisms underlying this association are not completely understood. METHODS: We analyzed messenger RNA (mRNA) microarray data from both invasive breast tumors (N = 602) and tumor-adjacent normal tissues (N = 508) from participants diagnosed with breast cancer in the Nurses' Health Study (NHS) and NHSII...
September 12, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28882676/malonylome-analysis-in-developing-rice-oryza-sativa-seeds-suggesting-that-protein-lysine-malonylation-is-well-conserved-and-overlaps-with-acetylation-and-succinylation-substantially
#12
Hana Mujahid, Xiaoxi Meng, Shihai Xing, Xiaojun Peng, Cailin Wang, Zhaohua Peng
In recent years, lysine malonylation has garnered wide spread interest due to its potential regulatory roles. While studies have been performed in bacteria, mouse, and human, the involvement and the biological function of this modification in plant are still largely unknown. We examined the global proteome profile of lysine malonylation in developing rice seeds using affinity enrichment followed by LC-MS/MS analysis. We identified 421 malonylated lysine sites across 247 proteins. Functional analyses showed predominant presence of malonylated proteins in metabolic processes, including carbon metabolism, glycolysis/gluconeogenesis, TCA cycle, as well as photosynthesis...
September 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28879687/recombinant-synthesis-of-hybrid-lipid-peptide-polymer-fusions-that-self-assemble-and-encapsulate-hydrophobic-drugs
#13
Kelli M Luginbuhl, Davoud Mozhdehi, Michael Dzuricky, Parisa Yousefpour, Fred C Huang, Nicholas R Mayne, Kristen Buehne, Ashutosh Chilkoti
Inspired by biohybrid molecules that are synthesized in Nature through post-translational modification (PTM), we have exploited a eukaryotic PTM to recombinantly synthesize lipid-polypeptide hybrid materials. By co-expressing yeast N-myristoyltransferase with an elastin-like polypeptide (ELP) fused to a short recognition sequence in E. coli, we show robust and high yield modification of the ELP with myristic acid. The ELP's reversible phase behavior is retained upon myristoylation and can be tuned to span a 30-60 °C...
September 6, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28860654/heterologous-expression-of-the-n-acetylglucosaminyltransferase-i-dictates-a-reinvestigation-of-the-n-glycosylation-pathway-in-chlamydomonas-reinhardtii
#14
Gaëtan Vanier, Pierre-Louis Lucas, Corinne Loutelier-Bourhis, Jessica Vanier, Carole Plasson, Marie-Laure Walet-Balieu, Philippe Chan Tchi-Song, Isabelle Remy-Jouet, Vincent Richard, Sophie Bernard, Azeddine Driouich, Carlos Afonso, Patrice Lerouge, Elodie Mathieu-Rivet, Muriel Bardor
Eukaryotic N-glycosylation pathways are dependent of N-acetylglucosaminyltransferase I (GnTI), a key glycosyltransferase opening the door to the formation of complex-type N-glycans by transferring a N-acetylglucosamine residue onto the Man5GlcNAc2 intermediate. In contrast, glycans N-linked to Chlamydomonas reinhardtii proteins arise from a GnTI-independent Golgi processing of oligomannosides giving rise to Man5GlcNAc2 substituted eventually with one or two xylose(s). Here, complementation of C. reinhardtii with heterologous GnTI was investigated by expression of GnTI cDNAs originated from Arabidopsis and the diatom Phaeodactylum tricornutum...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28827587/a-prospective-analysis-of-mucosal-microbiome-metabonome-interactions-in-colorectal-cancer-using-a-combined-mas-1hnmr-and-metataxonomic-strategy
#15
James Kinross, Reza Mirnezami, James Alexander, Richard Brown, Alasdair Scott, Dieter Galea, Kirill Veselkov, Rob Goldin, Ara Darzi, Jeremy Nicholson, Julian R Marchesi
Colon cancer induces a state of mucosal dysbiosis with associated niche specific changes in the gut microbiota. However, the key metabolic functions of these bacteria remain unclear. We performed a prospective observational study in patients undergoing elective surgery for colon cancer without mechanical bowel preparation (n = 18). Using 16 S rRNA gene sequencing we demonstrated that microbiota ecology appears to be cancer stage-specific and strongly associated with histological features of poor prognosis...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28775968/the-role-of-s-palmitoylation-of-the-human-glucocorticoid-receptor-hgr-in-mediating-the-nongenomic-glucocorticoid-actions
#16
Nicolas C Nicolaides, Tomoshige Kino, Michael L Roberts, Eleni Katsantoni, Amalia Sertedaki, Paraskevi Moutsatsou, Anna-Maria G Psarra, George P Chrousos, Evangelia Charmandari
BACKGROUND: Many rapid nongenomic glucocorticoid actions are mediated by membrane-bound glucocorticoid receptors (GRs). S-palmitoylation is a lipid post-translational modification that mediates the membrane localization of some steroid receptors. A highly homologous amino acid sequence (663YLCM KTLLL671) is present in the ligand-binding domain of hGRα, suggesting that hGRα might also undergo S-palmitoylation. AIM: To investigate the role of the motif 663YLCMKTLLL671 in membrane localization of the hGRα and in mediating rapid nongenomic glucocorticoid signaling...
2017: Journal of Molecular Biochemistry
https://www.readbyqxmd.com/read/28743627/characterization-of-a-novel-non-receptor-tyrosine-kinase-src-from-litopenaeus-vannamei-and-its-response-to-white-spot-syndrome-virus-infection
#17
Defu Yao, Lingwei Ruan, Jingxiang Xu, Hong Shi, Xun Xu
Src family kinases (SFKs), a class of non-receptor tyrosine kinases, mediate a wide aspect of cellular signaling pathways that regulate cell proliferation, differentiation, motility and survival. In this study, we identified and characterized for the first time a novel SFK homologue from Litopenaeus vannamei (designated as LvSrc). Sequence analysis showed that LvSrc had a high homology with the identified SFKs, especially those from invertebrates. LvSrc contained the conserved SH3, SH2 and tyrosine kinase domains, as well as the potential phosphorylation and lipid modification sites...
July 23, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28694077/molecular-adaptation-to-high-pressure-in-cytochrome-p450-1a-and-aryl-hydrocarbon-receptor-systems-of-the-deep-sea-fish-coryphaenoides-armatus
#18
Benjamin Lemaire, Sibel I Karchner, Jared V Goldstone, David C Lamb, Jeffrey C Drazen, Jean François Rees, Mark E Hahn, John J Stegeman
Limited knowledge of the molecular evolution of deep-sea fish proteomes so far suggests that a few widespread residue substitutions in cytosolic proteins binding hydrophilic ligands contribute to resistance to the effects of high hydrostatic pressure (HP). Structure-function studies with additional protein systems, including membrane bound proteins, are essential to provide a more general picture of adaptation in these extremophiles. We explored molecular features of HP adaptation in proteins binding hydrophobic ligands, either in lipid bilayers (cytochrome P450 1A - CYP1A) or in the cytosol (the aryl hydrocarbon receptor - AHR), and their partners P450 oxidoreductase (POR) and AHR nuclear translocator (ARNT), respectively...
July 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28691019/fish-oil-feeding-modulates-the-expression-of-hepatic-micrornas-in-a-western-style-diet-induced-nonalcoholic-fatty-liver-disease-rat-model
#19
Hualin Wang, Yang Shao, Fahu Yuan, Han Feng, Na Li, Hongyu Zhang, Chaodong Wu, Zhiguo Liu
Nonalcoholic fatty liver disease (NAFLD) is one of the most prevalent chronic liver diseases worldwide. Recent studies have indicated that fish oil supplementation has benefits against NAFLD. Our previous transcriptomic study has validated the effect of fish oil supplementation on altering hepatic gene expression in a NAFLD rat model. In the current study, we examined the effects of fish oil on the expression of hepatic microRNAs. Male Sprague-Dawley rats were fed with a lab chow (CON), high-fat high-cholesterol diet (WD), or WD supplemented with fish oil (FOH), respectively...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28686452/immunostimulatory-properties-of-lipid-modified-cpg-oligonucleotides
#20
Chunsong Yu, Myunggi An, Meng Li, Haipeng Liu
Innate immune responses recognizing pathogen associated molecular patterns play important roles in adaptive immunity. As such, ligands which mimic the conserved products of microbial and activate innate immunity are widely used as adjuvants for vaccines. Synthetic single strand oligodeoxynucleotides (ODNs) containing unmethylated cytosine-guanine (CpG) motifs which bind Toll-like receptor 9 (TLR9) are powerful molecular adjuvants, potentiating both humoral and cellular responses. However, CpG ODN's in vitro potency has not been translated to in vivo settings primarily due to issues associated with delivery and toxicity...
August 7, 2017: Molecular Pharmaceutics
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