MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming

Hirosawa, Makoto; Hoshida, Masaki; Ishikawa, Masato; Toya, Tomoyuki

doi:10.1093/bioinformatics/9.2.161

Cited by 138 publications

(133 citation statements)

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“…Data was acquired using an automatic information-dependent acquisition system (Applied Biosystems), which locates the most intense ions in a TOF MS spectrum and performs an optimized MS/MS analysis on the selected ions. The product ion spectra generated by nanoscale capillary LC-MS/MS were searched against National Center for Biotechnology Information databases for exact matches using the ProID (Applied Biosystems) and MASCOT search programs 40 . A Homo sapiens taxonomy restriction was used, and the mass tolerance of both precursor ions and fragment ions was set to ± 0.3 Da.…”

Section: Nanoelectrospray Mass Spectrometrymentioning

confidence: 99%

ERK promotes tumorigenesis by inhibiting FOXO3a via MDM2-mediated degradation

et al. 2008

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The RAS-ERK pathway is known to play a pivotal role in differentiation, proliferation and tumour progression. Here, we show that ERK downregulates Forkhead box O 3a (FOXO3a) by directly interacting with and phosphorylating FOXO3a at Ser 294, Ser 344 and Ser 425, which NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript consequently promotes cell proliferation and tumorigenesis. The ERK-phosphorylated FOXO3a degrades via an MDM2-mediated ubiquitin-proteasome pathway. However, the nonphosphorylated FOXO3a mutant is resistant to the interaction and degradation by murine double minute 2 (MDM2), thereby resulting in a strong inhibition of cell proliferation and tumorigenicity. Taken together, our study elucidates a novel pathway in cell growth and tumorigenesis through negative regulation of FOXO3a by RAS-ERK and MDM2.The constitutive activation of certain signal transduction cascades leads to the development of tumours and the resistance of tumours to clinical therapy 1,2 . The RAS-ERK pathway triggers one of these cascades and governs many important functions, such as cell fate, differentiation, proliferation and survival in invertebrate and mammalian cells 3,4 . Human tumours frequently overexpress RAS or harbour activated RAS with a point mutation, which contributes substantially to tumour cell growth, invasion and angiogenesis 1, 2 , 5 -8. Cell plasma membrane receptor tyrosine kinases activate RAS GTPases, and GTP-bound RAS activates A-RAF, B-RAF and RAF-1 (ref. 10,17,18,21 , but the E3 ubiquitin ligase responsible for FOXO3a degradation has yet to be identified. MDM2, an E3 ubiquitin ligase plays an important role in the development of multiple human cancers through degrading tumour suppressor proteins, such as p53, RB and E-cadherin [22][23][24][25] . In addition, MDM2 has been shown to be regulated by the RAS-ERK signalling pathway 26 and blocking ERK activity with an MEK1 inhibitor, U0126, reduces MDM2 expression in breast cancer cells 27 .Here, we identify a novel pathway involving the downregulation of FOXO3a expression by RAS-ERK and MDM2, which leads to promotion of cell growth and tumorigenesis. We show that ERK interacts with and phosphorylates FOXO3a at Ser 294, Ser 344 and Ser 425; phosphorylation of FOXO3a at these residues increases FOXO3a-MDM2 interaction and enhances FOXO3a degradation via an MDM2-dependent ubiquitin-proteasome pathway. The non-phosphorylated FOXO3a-mimic mutant, compared to the phosphorylated FOXO3a-mimic mutant, exhibits more resistance to the interaction and degradation by MDM2, resulting in a strong inhibition of cell proliferation in vitro and tumorigenesis in vivo. RESULTS ERK suppresses FOXO3a stability and induces its nuclear exclusionThe RAS-ERK is an essential oncogenic signalling cascade that promotes tumour cell growth and development 8,28 . It was known that other oncogenic kinases, AKT and IKK, (Fig. 1b, c). Similarly, using Erk small interference RNA (siRNA) to knockdown ERK protein expression level in HeLa cells (Fig. 1d), or trea...

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Section: Nanoelectrospray Mass Spectrometrymentioning

confidence: 99%

ERK promotes tumorigenesis by inhibiting FOXO3a via MDM2-mediated degradation

et al. 2008

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“…Data analysis methods were also investigated for protein identification either on the basis of database search algorithm with software such as SEQUEST (Diament and Noble, 2011) or MASCOT (Hirosawa et al, 1993;Kocher et al, 2011), spectral library searches (Desiere et al, 2006;Jones et al, 2006;Lam et al, 2007;Vizcaino et al, 2009;Yates et al, 1998), de novo sequencing (Cox and Mann, 2009;Frank and Pevzner, 2005;Tabb et al, 2008;Zhang et al, 2012), or with hybrid strategies (Mann and Wilm, 1994;Tabb et al, 2003Tabb et al, , 2007.…”

Section: Methodsmentioning

confidence: 99%

Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology

Longuespée

Fléron

Pottier

et al. 2014

OMICS: A Journal of Integrative Biology

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“…Flow through fractions containing the low or high affinity peptides were subjected to Mass Spectrometry using an Eksigent nano-LC Ultra 2D HPLC coupled to an Orbitrap ion trap (Thermo Fischer, Waltham, Massachusetts, USA) providing a very high mass accuracy (< 5 ppm). Mascot software [13] incorporating the IPI human and the respective decoy databases was used to carry out database queries.…”

Section: Characterization Of Hla-b*44-derived Peptidesmentioning

confidence: 99%

Differential Impact of HLA-B*44 Allelic Mismaches at Position 156 on Peptide Binding Specificities and T-Cell Diversity

Badrinath¹,

Huyton

Kunze‐Schumacher³

et al. 2014

J Stem Cell Res Ther

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The molecular understanding of how we can mismatch patients and donors and still have successful clinical outcomes will help to guide the future of unrelated bone-marrow transplantation.Single amino acid mismatches at position 156 on the alpha 2 helix of B*44 variants have been described to cause immunological episodes. The magnitude of permissivity between B44/156 variants differs from peptide presentation independent of the peptide loading complex (B*44:28) to influencing clinical episodes (B*44:02 vs. B*44:03). We here investigated if the single exchange of an Asp>Glu as occurring in B*44:35 at residue 156 would force an immune response in vitro.We developed an in vitro system by recombinant co-expression of a single membrane-bound allogeneic HLA class I molecule in donor cells and co-incubating these cells with autologous T-cells. This strategy enables the study of single HLA class I mismatches and excludes the influence of minor antigens. We found these T-cells to be able to differentially discriminate between mismatched B*44 subtypes and their micropolymorphism. To understand how certain pHLA landscapes shaping the alloreactive immune response, we sequenced the individual peptides derived from B*44/156 subtypes using LC-ESI-MS/MS technology. Based on the peptide data we modeled the structure of the B*44:35 variant and can describe the unexpected immunological reaction of the mismatched B*44 subtypes through structural manipulation of the heavy chain.The meticulous characterization of peptide-binding profiles for key alleles, as well as the evaluation of T-cell responses and structural analysis in the context of one-allele mismatches will open the door to a new era in bonemarrow transplantation.

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MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming

Cited by 138 publications

References 0 publications

ERK promotes tumorigenesis by inhibiting FOXO3a via MDM2-mediated degradation

ERK promotes tumorigenesis by inhibiting FOXO3a via MDM2-mediated degradation

Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology

Differential Impact of HLA-B*44 Allelic Mismaches at Position 156 on Peptide Binding Specificities and T-Cell Diversity

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