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  • 1
    Publication Date: 2013-02-02
    Description: Microscopy and mass spectrometry (MS) are complementary techniques: The former provides spatiotemporal information in living cells, but only for a handful of recombinant proteins at a time, whereas the latter can detect thousands of endogenous proteins simultaneously, but only in lysed samples. Here, we introduce technology that combines these strengths by offering spatially and temporally resolved proteomic maps of endogenous proteins within living cells. Our method relies on a genetically targetable peroxidase enzyme that biotinylates nearby proteins, which are subsequently purified and identified by MS. We used this approach to identify 495 proteins within the human mitochondrial matrix, including 31 not previously linked to mitochondria. The labeling was exceptionally specific and distinguished between inner membrane proteins facing the matrix versus the intermembrane space (IMS). Several proteins previously thought to reside in the IMS or outer membrane, including protoporphyrinogen oxidase, were reassigned to the matrix by our proteomic data and confirmed by electron microscopy. The specificity of peroxidase-mediated proteomic mapping in live cells, combined with its ease of use, offers biologists a powerful tool for understanding the molecular composition of living cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916822/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916822/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhee, Hyun-Woo -- Zou, Peng -- Udeshi, Namrata D -- Martell, Jeffrey D -- Mootha, Vamsi K -- Carr, Steven A -- Ting, Alice Y -- DP1 OD003961/OD/NIH HHS/ -- P30 CA014051/CA/NCI NIH HHS/ -- R01 GM077465/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Mar 15;339(6125):1328-31. doi: 10.1126/science.1230593. Epub 2013 Jan 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23371551" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ascorbate Peroxidases/*genetics ; Biotinylation ; COS Cells ; Cercopithecus aethiops ; Gene Targeting/*methods ; Genetic Engineering ; HEK293 Cells ; Humans ; Mass Spectrometry ; Mitochondria/*metabolism ; Proteomics/*methods
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-07-02
    Description: Lenalidomide is a highly effective treatment for myelodysplastic syndrome (MDS) with deletion of chromosome 5q (del(5q)). Here, we demonstrate that lenalidomide induces the ubiquitination of casein kinase 1A1 (CK1alpha) by the E3 ubiquitin ligase CUL4-RBX1-DDB1-CRBN (known as CRL4(CRBN)), resulting in CK1alpha degradation. CK1alpha is encoded by a gene within the common deleted region for del(5q) MDS and haploinsufficient expression sensitizes cells to lenalidomide therapy, providing a mechanistic basis for the therapeutic window of lenalidomide in del(5q) MDS. We found that mouse cells are resistant to lenalidomide but that changing a single amino acid in mouse Crbn to the corresponding human residue enables lenalidomide-dependent degradation of CK1alpha. We further demonstrate that minor side chain modifications in thalidomide and a novel analogue, CC-122, can modulate the spectrum of substrates targeted by CRL4(CRBN). These findings have implications for the clinical activity of lenalidomide and related compounds, and demonstrate the therapeutic potential of novel modulators of E3 ubiquitin ligases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kronke, Jan -- Fink, Emma C -- Hollenbach, Paul W -- MacBeth, Kyle J -- Hurst, Slater N -- Udeshi, Namrata D -- Chamberlain, Philip P -- Mani, D R -- Man, Hon Wah -- Gandhi, Anita K -- Svinkina, Tanya -- Schneider, Rebekka K -- McConkey, Marie -- Jaras, Marcus -- Griffiths, Elizabeth -- Wetzler, Meir -- Bullinger, Lars -- Cathers, Brian E -- Carr, Steven A -- Chopra, Rajesh -- Ebert, Benjamin L -- P01 CA066996/CA/NCI NIH HHS/ -- P01CA108631/CA/NCI NIH HHS/ -- R01 HL082945/HL/NHLBI NIH HHS/ -- R01HL082945/HL/NHLBI NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- T32GM007753/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Jul 9;523(7559):183-8. doi: 10.1038/nature14610. Epub 2015 Jul 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Brigham and Women's Hospital, Division of Hematology, Boston, Massachusetts 02115, USA [2] University Hospital of Ulm, Department of Internal Medicine III, 89081 Ulm, Germany [3] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Brigham and Women's Hospital, Division of Hematology, Boston, Massachusetts 02115, USA [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; Celgene Corporation, San Diego, California 92121, USA. ; Brigham and Women's Hospital, Division of Hematology, Boston, Massachusetts 02115, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; Roswell Park Cancer Institute, Buffalo, New York 14263, USA. ; University Hospital of Ulm, Department of Internal Medicine III, 89081 Ulm, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26131937" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Casein Kinase I/genetics/*metabolism ; Cell Line ; Gene Expression Regulation/drug effects ; HEK293 Cells ; Humans ; Immunologic Factors/pharmacology ; Jurkat Cells ; K562 Cells ; Mice ; Molecular Sequence Data ; Myelodysplastic Syndromes/*genetics/*physiopathology ; Peptide Hydrolases/chemistry ; Proteolysis/drug effects ; Sequence Alignment ; Sequence Deletion ; Species Specificity ; Thalidomide/*analogs & derivatives/pharmacology ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination/*drug effects
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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