Motif-centric phosphoproteomics to target kinase-mediated signaling pathways

細胞内リン酸化修飾の大規模計測に成功 --極微量試料からのリン酸化経路解析も可能に--. 京都大学プレスリリース. 2022-02-01.Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7, 000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner

REMOVAL OF DISSOLVED METAL IONS BY BIOGENIC MANGANESE OXIDES PRODUCED BY ENRICHMENT CULTURES OF MANGANESE-OXIDIZING BACTERIA

Joint Research on Environmental Science and Technology for the Eart

MFH-1 is required for bone morphogenetic protein-2-induced osteoblastic differentiation of C2C12 myoblasts

AbstractMesenchyme forkhead-1 (MFH-1), a winged helix/forkhead transcription factor, is expressed in developing cartilaginous tissues, kidney and arch arteries, and is essential for the normal development of the axial skeleton and aortic arch formation of mice. To investigate the possible role of MFH-1 in osteogenesis and osteoblast differentiation, we examined expression of MFH-1 induced by bone morphogenetic protein-2 (BMP-2) in C2C12 myoblasts, and found that MFH-1 protein and also MFH-1 mRNA increased markedly in C2C12 cells after treatment with BMP-2. To confirm the hypothesis that BMP-2 induced osteoblastic differentiation of C2C12 cells by increasing MFH-1 expression, we lowered the endogenous MFH-1 level by stably transfecting C2C12 cells with antisense MFH-1 sequence, and found that in antisense MFH-1 cell lines, both alkaline phosphatase (ALP) activity and production of osteocalcin induced by BMP-2 decreased markedly in comparison with control cell lines. Our results suggest that the BMP-2-induced MFH-1 protein may play a key role in regulating the commitment to osteoblastic differentiation of C2C12 myoblasts and production of osteoblast markers including ALP and osteocalcin

HybGFS: a hybrid method for genome-fingerprint scanning

BACKGROUND: Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS/MS) database searching. However, these methods cannot identify proteins that are not already listed in existing databases. Moreover, the alternative approach of de novo sequencing requires costly equipment and the interpretation of complex MS/MS spectra. Thus, there is a need for novel high-throughput protein-identification methods that are independent of existing predefined protein databases. RESULTS: Here, we present a hybrid method for genome-fingerprint scanning, known as HybGFS. This technique combines genome sequence-based peptide MS/MS ion searching with liquid-chromatography elution-time (LC-ET) prediction, to improve the reliability of identification. The hybrid method allows the simultaneous identification and mapping of proteins without a priori information about their coding sequences. The current study used standard LC-MS/MS data to query an in silico-generated six-reading-frame translation and the enzymatic digest of an entire genome. Used in conjunction with precursor/product ion-mass searching, the LC-ETs increased confidence in the peptide-identification process and reduced the number of false-positive matches. The power of this method was demonstrated using recombinant proteins from the Escherichia coli K12 strain. CONCLUSION: The novel hybrid method described in this study will be useful for the large-scale experimental confirmation of genome coding sequences, without the need for transcriptome-level expression analysis or costly MS database searching