Protein N-terminus Analysis Based Guanidination
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens Saccharomyces Cerevisiae
SUBMITTER: 
Lihua Zhang
PROVIDER: PXD015305 | iProX | Wed Sep 04 00:00:00 BST 2019
REPOSITORIES: iProX
Similar Datasets
Project description:We propose an isolation strategy based on a broad-spectrum antimicrobial epsilon-poly-L–lysine (ε-PL) to precipitate bacterial extracellular vesicles (BEVs) at a relatively low centrifugal speed (10,000 × g). Compared to the standard ultracentrifugation (UC) strategy, our method can enrich BEVs from large volumes of media inexpensively and rapidly. The precipitated BEVs can be recovered by adjusting pH and ionic strength of the media, followed by ultrafiltration step to remove ε-PL and achieve buffer exchange. To address whether BEVs isolated by these two methods lead to different host responses, we isolated Escherichia coli (E. coli) and Staphylococcus aureus BEVs from bacterial culture media using ultracentrifugation and our ε-poly- L-lysine-based method, respectively. Then we stimulated THP-1 cells with the isolated BEVs and the global transcript profiles were evaluated by the RNA-seq technique. Compared with the unstimulated THP-1 cells, BEV isolated by both methods could trigger a striking alteration in the gene expression pattern. Among the functions significantly enriched by these DEGs were immune response and leucocyte chemotaxis. The results indicated that the BEVs isolated by the ε-PL-based method also retained the in vitro biological activity as the commonly used ultracentrifugation.
2022-08-02 | GSE207009 | GEO
Project description:Small ubiquitin-like modifier (SUMO) typically conjugates to target proteins through isopeptide linkage to the ε-amino group of lysine residues. This posttranslational modification (PTM) plays pivotal roles in modulating protein function. As a key regulator of actin cytoskeleton dynamics, cofilins (CFLs) are well-known to undergo several different kinds of PTMs. Using mass spectrometry, our study identified the N-terminal α-amino group, rather than any of the ε-amino groups of the internal lysines, as the sole SUMO-conjugation site of cofilin-1 (CFL1).
2023-10-24 | PXD038392 | Pride
Project description:Both Gram-negative and Gram-positive bacteria can release vesicle-like structures referred as bacterial extracellular vesicles (BEVs), which contain various bioactive compounds. BEVs play important roles in the microbial community interactions and host-microbe interactions. Markedly, BEVs can be delivered to host cell, thus modulating the development and function of the innate immune system. To clarify the compositions and biological functions of BEVs, these vesicles need to be collected with high purity and bioactivity. Here we propose an isolation strategy based on a broad-spectrum antimicrobial epsilon-poly-L–lysine (ε-PL) to precipitate BEVs at a relatively low centrifugal speed (10,000 × g). Compared to the standard ultracentrifugation strategy, our method can enrich BEVs from large volumes of media inexpensively and rapidly. The precipitated BEVs can be recovered by adjusting pH and ionic strength of the media, followed by ultrafiltration step to remove ε-PL and achieve buffer exchange. Protein compositions of the BEVs enriched by ultracentrifugation and ε-PL-based method are measured using LC-MS/MS. The resultant data indicate that protein compositions of the ε-PL-precipitated BEVs are comparable to those purified by ultracentrifugation.
2022-08-03 | PXD034259 | Pride
Project description:The acetylation of amino groups within proteins is one of the major posttranslational modifications (PTMs) in all organisms. N-terminal acetyltransferases (NATs) or lysine acetyltransferases (KATs) catalyze the transfer of the acetyl group from the donor substrate acetyl coenzyme A (Ac-CoA) to the targeted amino group, which is either the α-amino groups of N-termini or the ε-amino group of internal lysine residues. In contrast to N-terminal acetylation (NTA), the acetylation of lysine residues (KA) is reversible, whereby lysine deacetylases (KDACs) are responsible for the removal of acetyl groups from proteins. Furthermore, KA occurs posttranslationally, whereas NTA is described mainly as a cotranslational modification with the exception for N-terminally processed proteins, which are imported to chloroplasts and mitochondria
2024-08-19 | PXD044167 | JPOST Repository
Project description:Comprehensive evaluation of human cell lines for the transcription dynamics in response to the inhibition of PKC isozymes ε & ζ in bladder cancer.
2024-10-30 | GSE245118 | GEO
Project description:Effective and convenient covalent protein conjugation could benefit diverse biological systems, stabilizing key protein protein interactions which are otherwise reversible. Neisseria meningitidis contains a protein which undergoes autoproteolysis via an anhydride. Here, we harness this spontaneously generated electrophile for covalent targeting of unmodified endogenous proteins. In ‘NeissLock’, a binding protein genetically fused to the self-processing module (SPM) docks to its target protein. Upon triggering with calcium, the aspartic anhydride generated at the C-terminus of the binding protein allows nucleophilic attack by nearby residues on the target protein, so ligating the proteins. We established a computational tool to search the Protein Data Bank, assessing proximity of amines to C-termini. We validated and optimized the NeissLock concept using the Ornithine Decarboxylase/Antizyme complex. A range of nucleophiles on the target (α-amine or ε-amines) could rapidly react with the anhydride, but reaction was blocked if the partner protein did not dock. Surprisingly, the optimal pH for covalent ligation was 7.0. We then armed Transforming Growth Factor-α with SPM and established covalent targeting to Epidermal Growth Factor Receptor at the surface of living cells. NeissLock harnesses exceptional protein chemistry to allow covalent targeting of endogenous proteins under mild conditions with up to 80% yield, allowing new possibilities for molecular engineering.
2021-02-01 | PXD023073 | Pride
Project description:Investigation of the function of human alpha-cells remains a challenge due to the lack of simple and cost-effective purification methods to isolate high-quality alpha-cells from islets. Here, we introduce a novel and simple method for enriching live alpha-cells from dissociated human islet cells by using the reaction-based probe diacetylated Zinpyr1 (DA-ZP1) with > 97% purity.
2023-09-29 | GSE199412 | GEO
Project description:We report the difference of genome-wide chromatin profiling of histone modifications in mammalian cells after PBS or LPS treatment. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse peritoneal macrophages. We find that lysine 4 and lysine 9 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential.Trimethylation of lysine 9 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of mammalian cells after LPS treatment.
2019-08-04 | GSE102252 | GEO
Project description:ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by S. albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering. Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18. Our results show that key genes in the glycolysis, glyoxylate, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. Furthermore, transcriptional and translational upregulation of genes involved in the tricarboxylic acid cycle, oxidative phosphorylation, and pentose phosphate pathway also increase the pools of available NADH, ATP, and NADPH. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure, thus further regulating the ε-PL biosynthesis. This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing a theoretical foundation development of advanced Streptomycetaceae microbial cell factories.
2023-07-20 | PXD036099 | Pride
Project description:Array-based comparative genomic hybridisation is a high-resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array CGH. This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridised using a hybstation and analysed using BleuFuse feature extraction software, with over 95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA without the need for amplification or target reduction and a 90% reduction of Cot1-DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using “off-the-shelf” oligo-libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results. Keywords: comparative genomic hybridization, oligonucleotide,
2005-12-19 | GSE3264 | GEO