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lipid modification and sequencing

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https://www.readbyqxmd.com/read/29235492/proteome-wide-analysis-of-lysine-2-hydroxyisobutyrylation-in-developing-rice-oryza-sativa-seeds
#1
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
#2
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...
December 11, 2017: 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
#3
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
#4
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 characterized the CFAS-null and -overexpression mutants in L. mexicana, the causative agent for cutaneous leishmaniasis in Mexico and central America...
November 24, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/29140585/timap-the-versatile-protein-phosphatase-1-regulator-in-endothelial-cells
#5
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
#6
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...
November 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29042445/analysis-of-substrate-specificity-of-trypanosoma-brucei-osts-by-functional-expression-of-domain-swapped-chimeras-in-yeast
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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...
November 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28953347/highly-potent-antibacterial-organometallic-peptide-conjugates
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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...
January 6, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/28879687/recombinant-synthesis-of-hybrid-lipid-peptide-polymer-fusions-that-self-assemble-and-encapsulate-hydrophobic-drugs
#19
Kelli M Luginbuhl, Davoud Mozhdehi, Michael Dzuricky, Parisa Yousefpour, Fred C Huang, Nicholas R Mayne, Kristen L 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
#20
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
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