Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs

Obenauer, John C.

doi:10.1093/nar/gkg584

Cited by 1,497 publications

(1,399 citation statements)

References 22 publications

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“…This indicates that PKD recognizes phosphorylation sites with certain flexibility, rather than strictly adhering to the previously defined motif (e.g., a Scansite [23] search at low stringency did not identify c-jun Ser58 as a phosphorylation motif). Thus, future target predictions might consider sites with features similar to those presently identified in c-jun.…”

Section: Resultsmentioning

confidence: 99%

Identification of a novel phosphorylation site in c-jun directly targeted in vitro by protein kinase D

Waldron

Whitelegge

Faull

2007

Biochemical and Biophysical Research Communications

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Protein kinase D (PKD) phosphorylates the c-jun amino-terminal in vitro at site(s) distinct from JNK [C. Hurd, R.T. Waldron, E. Rozengurt, Protein kinase D complexes with c-jun N-terminal kinase via activation loop phosphorylation and phosphorylates the c-jun N-terminus, Oncogene 21 (2002) 2154-2160], but the sites have not been identified. Here, metabolic 32 P-labeling of c-jun protein in COS-7 cells indicated that PKD phosphorylates c-jun in vivo at a site(s) between aa 43-93, a region containing important functional elements. On this basis, the PKD-mediated phosphorylation site(s) was further characterized in vitro using GST-c-jun fusion proteins. PKD did not incorporate phosphate into Ser63 and Ser73, the JNK sites in GST-c-jun(1-89). Rather, PKD and JNK could sequentially phosphorylate distinct site(s) simultaneously. By mass spectrometry of tryptic phosphopeptides, Ser58 interposed between the JNK-binding portion of the delta domain and the adjacent TAD1 was identified as a prominent site phosphorylated in vitro by PKD. These data were further supported by kinase reactions using truncations or point-mutations of GST-c-jun. Together, these data suggest that PKD-mediated phosphorylation modulates c-jun at the level of its N-terminal functional domains.

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Section: Resultsmentioning

confidence: 99%

Identification of a novel phosphorylation site in c-jun directly targeted in vitro by protein kinase D

Waldron

Whitelegge

Faull

2007

Biochemical and Biophysical Research Communications

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“…A well-known downstream target of PI3K is the serine/threonine kinase, Akt, which transmits survival and proliferation signals from growth factors [27,28]. Numerous Akt substrates have been identified and validated [29]. Activated Akt phosphorylates target molecules that control key cellular processes such as apoptosis, cell cycle progression, transcription and translation.…”

Section: Discussionmentioning

confidence: 99%

Stem cell factor/c-Kit signaling in in vitro cultures supports early mouse embryonic development by accelerating proliferation via a mechanism involving Akt-downstream genes

Lim

Eum

Lee

et al. 2010

J Assist Reprod Genet

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Purpose Stem cell factor (SCF)/c-Kit regulates the proliferation and survival of germ cells or stem cells; however, little is known about the role of SCF/c-Kit in preimplantation embryo development. Methods Using exogenous SCF supplementation and c-Kit siRNA injection, we investigated the role and mechanism of SCF/c-Kit in pre-implantation mouse embryos.Results Addition of soluble SCF to the culture medium improved blastocyst formation. c-Kit gene silencing reduced the rate of blastocyst formation and delayed embryonic development. The number of proliferating cells in c-Kit gene-silenced blastocysts decreased, whereas the number of apoptotic cells in blastocysts obtained from both experimental and the control groups was not affected. RT-PCR, immunostaining and western blotting revealed that proliferation-related Akt downstream targets were substantially affected by c-Kit gene silencing. Conclusion SCF/c-Kit signaling through Akt downstream targets is likely involved in mediating the cleavage and proliferation of blastomeres during mouse pre-implantation embryogenesis.

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“…An analysis of human Rictor protein sequence with the Scansite algorithm (http://scansite.mit.edu) indicates that residue Thr1135, which we identified as a potential phosphorylation site, is a putative phosphorylation site for Akt/PKB at high stringency (Obenauer et al, 2003). The sequence of this site is NRRIRTLpTEPSV, which conforms to the Akt/PKB consensus motif, Arg-x-Argx-x-pSer/Thr (RxRxxpS/T, where x is any amino acid).…”

Section: Identification Of Phosphorylation Sites Within Rictormentioning

confidence: 99%

Rictor is a novel target of p70 S6 kinase-1

et al. 2009

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The rapamycin-insensitive companion of mammalian target of rapamycin (mTOR) (Rictor) is a key member of mTOR complex-2 (mTORC2), which phosphorylates the AGC kinases Akt/PKB, PKC and SGK1 at a C-terminal hydrophobic motif. We identified several novel sites on Rictor that are phosphorylated, including Thr1135, which is conserved across all vertebrates. Phosphorylation of this site on Rictor is stimulated by amino acids and growth factors through a rapamycin-sensitive signaling cascade. We demonstrate here that Rictor is a direct target of the ribosomal protein S6 kinase-1 (S6K1). Rictor phosphorylation at Thr1135 does not lead to major changes in mTORC2-kinase activity. However, phosphorylation of this site turns over rapidly and mediates 14-3-3 binding to Rictor and mTORC2, providing possibility for altered interactions of the complex. These findings reveal an unexpected signaling input into mTORC2, which is regulated by amino acids, growth factors and rapamycin.

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Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs

Cited by 1,497 publications

References 22 publications

Identification of a novel phosphorylation site in c-jun directly targeted in vitro by protein kinase D

Identification of a novel phosphorylation site in c-jun directly targeted in vitro by protein kinase D

Stem cell factor/c-Kit signaling in in vitro cultures supports early mouse embryonic development by accelerating proliferation via a mechanism involving Akt-downstream genes

Rictor is a novel target of p70 S6 kinase-1

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