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Expression Data from Escherichia coli grown to mid-log growth phase.

ABSTRACT: B-methylthiolation of the Escherichia coli Ribosomal Protein S12 Regulates Anaerobic Gene Expression. B-methylthiolation is a unique post-translational modification (PTM) that maps to a conserved Asp 88 of the bacterial ribosomal protein S12. This modification is phylogenetically conserved in several bacteria yet has not been identified on other proteins.

ORGANISM(S): Escherichia coli

PROVIDER: GSE21551 | GEO | 2010/05/07

SECONDARY ACCESSION(S): PRJNA126219

REPOSITORIES: GEO

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Expression Data from Escherichia coli grown to mid-log growth phase.

Project description:B-methylthiolation of the Escherichia coli Ribosomal Protein S12 Regulates Anaerobic Gene Expression. B-methylthiolation is a unique post-translational modification (PTM) that maps to a conserved Asp 88 of the bacterial ribosomal protein S12. This modification is phylogenetically conserved in several bacteria yet has not been identified on other proteins. We use microarrays to delineate the association of prokaryotic ribosomal protein PTM to the regulation of genes.

2010-05-27 | E-GEOD-21551 | biostudies-arrayexpress

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells. 2 histone marks (pan-lysine acetylation and pan-lysine crotonylation) were studied in 1 human cell type and 2 mouse cell types using ChIP-Seq. Input was sequenced for each cell type as a control. Pan-anti_Kac and pan-anti_Kcr antibodies were custom developed with PTM BioLab, Co., Ltd (Chicago, IL).

2011-10-06 | E-GEOD-32663 | biostudies-arrayexpress

Combinatorial effect of ARTP mutagenesis and ribosome engineering on an industrial Streptomyces albus strain S12 for enhanced biosynthesis of salinomycin

Project description:Streptomyces albus S12, TK and Tet30Chl25 are the parental strain , low-yield and high-yield of salinomycin mutant obtained by ARTP and ribosome engineering ,respectively. There are total 1602 differentially expressed genes (DEGs) show differences in expression between the mutant strain TK, Tet30Chl25 and the initial strain S12. KEGG pathway analysis of differentially expressed genes (DEGs) between the mutant strain TK, Tet30Chl25 and the initial strain S12 show that the relevant differential pathways affecting salinomycin production were mainly related to butanoate metabolism, starch and sucrose metabolism, glyoxylate metabolism. Besides , the transcription of genes in the salinomycin biosynthesis gene cluster and the transcription level of related genes in the precursors biosynthesis pathway were more active in the high-yield salinomycin production strain Tet30Chl25. Furthermore, the transcription level ribosomal protein, string response, two component system and sigma factors are more active in high-yield of salinomycin mutants and that may involve in regulation of salinomycin biosynthesis and may account for the high-yield of salinomycin.

2019-10-01 | GSE133580 | GEO

Global Identification of Protein PTMs in a Single-pass Database Search

Project description:Bottom-up proteomics database search algorithms used for peptide identification cannot comprehensively identify posttranslational modifications (PTMs) in a single-pass because of high false discovery rates (FDRs). A new approach to database searching enables Global PTM (G-PTM) identification by exclusively looking for curated PTMs, thereby avoiding the FDR penalty experienced during conventional variable modification searches. We identified nearly 2500 unique, high-confidence modified peptides comprising 31 different PTM types in single-pass database searches. Male C57BL/6J (B6) and CAST/EiJ (CAST) mice were purchased from The Jackson Laboratories (Bar Harbor, Maine) and housed in an environmentally controlled vivarium at the University of Wisconsin Biochemistry Department. Mice were provided standard rodent chow (Purina no. 5008) and water ad libitum, and maintained on a 12-hour light/dark cycle (6 AM – 6 PM). At 10 weeks of age, mice were sacrificed by CO2 asphyxiation. All animal procedures were preapproved by the University of Wisconsin Animal Care and Use Committee.

2015-07-31 | E-GEOD-59956 | biostudies-arrayexpress

Global Identification of Protein PTMs in a Single-pass Database Search

2015-07-31 | GSE59956 | GEO

Multi-omics approaches for revealing the epigenetic regulation of histone H3.1 during spermatogonial stem cell differentiation in vitro

Project description:Epigenetic regulation, particularly histone post translational modification (PTM), participates in spermatogonial stem cells (SSCs) differentiation. However, prior research is still limited to a single PTM. Herein, we constructed over 100 histone H3.1 targeted modification peptides, in combination with histone H3.1 modification binding protein identification, and RNA-Seq. We identified 7 differentially expressed histone H3.1 modifications. In addition, we selected H3K9me2 and H3S10ph for subsequent biotinylating peptide pull-down experiments, and identified a series of transcription factors, such as, GTF2E2 and SUPT5H, which appear to be crucial for the early SSC differentiation process.

2023-03-01 | GSE222617 | GEO

Pairwise comparison stationary phase vs mid-log

Project description:A pairwise comparison was performed between stationary phase specific samples and mid-log samples using four replicates and dye-swaps

2005-04-15 | E-UMCU-13 | biostudies-arrayexpress

Expression signatures of human HeLa cells with RNAi targetting A1 hnRNP, FUS, H hnRNP and p68-DDX5

Project description:Transcription profiling of human HeLa cells (cervical cancer cell line) transfected with a plasmid expressing shRNAs cloned into the pSuper expression vector compared to emprty vector negative controls for transfection. Four different RNA interference treatments targetted: A1 hnRNP (HNRNPA1, Heterogeneous nuclear ribonucleoprotein A1); FUS (fusion gene, involved in t(12;16) in malignant liposarcoma); H hnRNP (HNRNPH1); and p68 helicase (DDX5, DEAD (Asp-Glu-Ala-Asp) box polypeptide 5). Keywords: genetic modification

2008-08-20 | GSE12058 | GEO

Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide

Project description:Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide

| PRJNA791217 | ENA

Actin R256 mono-methylation is a conserved post-translational modification involved in transcription

Project description:Nuclear actin has been elusive due to the lack of molecular mechanisms. From actin-containing chromatin remodeling complexes, we discovered an arginine mono-methylation mark on evolutionarily conserved R256 residue of actin (R256me1). Actin R256 mutations in yeast affect nuclear functions, and cause diseases in human. Interestingly, we show that an antibody specific for actin R256me1 preferentially stain nuclear actin over cytoplasmic actin in yeast, mouse and human cells. We also show that actin R256me1 is regulated by protein arginine methyl transferase-5 (PRMT5) in HEK293 cells. Genome-wide survey of actin R256me1 mark provides a landscape for nuclear actin correlated with transcription. Further gene expression and protein interaction studies uncover extensive correlations between actin R256me1 and active transcription. The discovery of actin R256me1 mark suggests a fundamental mechanism to distinguish nuclear actin from cytoplasmic actin through post-translational modification (PTM), and potentially implicates an actin PTM mark in transcription and human diseases.

2020-08-26 | GSE156817 | GEO

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