Project description:Human Hsp90β is constitutively phosphorylated in vivo on two serine residues in the charged linker region, S226 and S255. We developed a targeted method to measure the phosphorylation occupancy (the extent of phosphorylation) of both phosphosites in a range of cultured cell lines and consistently found high occupancy (>90%) in the cytoplasm and nucleus. However, we found decreased phosphorylation, especially for S255, in Hsp90β purified from the conditioned medium of cultured K562 cells. In addition, we investigated if various cell growth conditions known to impact Hsp90β activity had an effect on the phosphorylation status of S226 and S255, but none of the conditions tested (e.g. heat shock, Hsp90β inhibition) resulted in an alteration of S226 and S255 phosphorylation.
Project description:Many archetypal and emerging classes of small-molecule therapeutics form covalent 38 protein adducts. In vivo, both the resulting conjugates and their off-target side conjugates have the potential to elicit antibodies, with implications for allergy and drug sequestration. Although β-lactam antibiotics are a drug class long associated with these immunological phenomena, the molecular underpinnings of off-target drug protein conjugation and consequent drug-specific immune responses remain incomplete. Here, using the classical β-lactam penicillin G (PenG) we have now probed the B and T cell determinants of drug-specific IgG responses to such conjugates in mice. Deep clonotyping reveals a dominant murine clonal antibody class encompassing phylogenetically-related IGHV1, IGHV5 and IGHV10 subgroup gene segments. Protein NMR and x-ray structural analyses reveal that these drive structurally convergent binding modes in adduct-specific antibody clones. Their common primary recognition mechanisms of the penicillin side-chain moiety (phenylacetamide in PenG)—regardless of CDRH3 length—limits cross-reactivity against other β-lactam antibiotics. This immunogenetics-guided discovery of the limited binding solutions available to antibodies against side products of an archetypal covalent inhibitor now suggests future potential strategies for the ‘germline-guided reverse engineering’ of such drugs away from unwanted immune responses.
Project description:To determine the modulation of gene expression of Leishmania mexicana(M379)-inoculated BALB/c ears in the presence of promastigote secretory gel (PSG) A genome-wide transcriptional analysis was performed by comparing the gene expression profiles of Leishmania mexicana- inoculated BALB/c ears and Leishmania mexicana plus PSG BALB/c ears. Leishmania mexicana amastigotes were purified from mouse cutaneous lesions and transformed in vitro in metacycic promastigotes (MT). After 6, 24 and 48 hours, ears were collected and processed for RNA extraction. Three Biological replicates per condition were run.
Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.
Project description:We used Illumina sequencing of poly-A selected RNA of Leishmania mexicana (WHO strain MNYC/BZ/62/M379) culture-adapted promastigotes (PRO), axenic amastigotes (AXA) and intracellular amastigotes (AMA) in mouse bone marrow derived macrophages (BMDM), 24h after infection, to map 5' and 3' ends of Leishmania transcripts and determine transcript abundances. The AMA samples were prepared from total RNA of infected macrophages thus containing a mixture of leishmanial and murine RNA transcripts. We also sequenced poly-A selected RNA from uninfected BMDMs. Three biological replicates per sample.
Project description:Protein phosphorylation by kinases regulates mammalian cell functions, such as growth, division, and signal transduction. Among human kinases, NME1 and NME2 are associated with metastatic tumor suppression, but remain understudied due to the lack of tools to monitor their cellular substrates. In particular, NME1 and NME2 are multi-specificity kinases phosphorylating serine, threonine, histidine, and aspartic acid residues of substrates, and the heat and acid sensitivity of phosphohistidine and phosphoaspartate complicates substrate discovery and validation. To provide new substrate monitoring tools, we established the γ-phosphate modified ATP analog, ATP-biotin, as a cosubstrate for phosphorylbiotinylation of NME1 and NME2 cellular substrates. Building upon this ATP-biotin compatibility, the Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS) method enabled validation of a known substrate and the discovery of seven NME1 and three NME2 substrates. Given the paucity of methods to study kinase substrates, ATP-biotin and the K-BILDS method are valuable tools to characterize the roles of NME1 and NME2 in human cell biology.
Project description:Chromatin insulators are DNA-protein complexes situated throughout the genome capable of demarcating independent transcriptional domains. Previous studies point to an important role for RNA in gypsy chromatin insulator function in Drosophila; however, the identity of these putative insulator-associated RNAs is not currently known. Here we utilize RNA-immunoprecipitation and high throughput sequencing (RIP-seq) to isolate RNAs stably associated with gypsy insulator complexes. Strikingly, these RNAs correspond to specific sense-strand, spliced, and polyadenylated mRNAs, including two insulator protein transcripts. In order to assess the functional significance of these associated mRNAs independent of their coding function, we expressed untranslatable versions of these transcripts in developing flies and observed both alteration of insulator complex nuclear localization as well as improvement of enhancer-blocking activity. Together these data suggest a novel, noncoding mechanism by which certain mRNAs contribute to chromatin insulator function. RIP-seq of insulator proteins with different library preparations and multiple biological replicates
Project description:To identify genes underpinning the antagonistic effects of extracellular ATP on programmed cell death induced by fumonisin B1 (FB1), we conducted a kinetic DNA microarray experiment using samples harvested in the critical time window when exogenous ATP is known to suppress cell death. Arabidopsis cell suspension cultures were treated with FB1 at time = 0 h and exogenous ATP added at time = 40 h. Differential gene expression analysis using microarrays was performed on samples harvested at 41, 42, 44, and 48 h.
Project description:The acylated pore-forming Repeats in ToXin (RTX) cytolysins α-hemolysin (HlyA) and adenylate cyclase toxin (CyaA) bind primarily to β2 integrins of leukocytes. HlyA binds the common CD18 subunit of the β2 integrins and CyaA selectively binds the CD11b subunit of complement receptor 3 (CR3). However, both toxins can also bind and permeabilize membranes of a variety of nonmyeloid cells. We constructed HlyA1-563/CyaA860-1706 hybrid molecules activated by the CyaA-activating acyltransferase CyaC, or by the HlyA-activating acyltransferase HlyC. We show that the C-terminal portion of the HlyA molecule, comprising the acylated segment and the RTX domain (residues 564 to 1024), can be functionally swapped with the CyaC-activated acylated segment bearing palmitoylated Lys983 and the much larger RTX domain of CyaA. Compared to the CD18-interacting HlyA, the CR3-interacting HlyA1-563/CyaA860-1706 hybrid exhibited a selectively reduced cytotoxicity on human THP-1 monocytes and Chinese hamster ovary (CHO) cells expressing CR3 (CHO-CR3) or lymphocyte function-associated antigen 1 (CHO-LFA1). However, the mono-palmitoylated HlyA1-563/CyaA860-1706 hybrid remained fully hemolytic and cytolytic toward erythrocytes and mock-transfected CHO cells and exhibited a comparable membrane activity on artificial planar lipid membranes as the bi-myristoylated HlyA. Thus, regardless of the length or number of the attached fatty acyl chains, the CyaC-activated HlyA1-563/CyaA860-1706 hybrid and the intact HlyA were comparably active on cells or artificial membranes lacking β2 integrins. These data suggest that once the hydrophobic pore-forming domain comprising N-terminal half of HlyA is brought into close contact with the cell membrane by the mono-palmitoylated acylated segment of CyaA, it can efficiently form fully cytolytic HlyA-like membrane pores.