TY - JOUR

T1 - Proteomic analyses reveal divergent ubiquitylation site patterns in murinetissues

AU - Wagner, Sebastian A

AU - Beli, Petra

AU - Weinert, Brian T

AU - Schölz, Christian Friedhold

AU - Kelstrup, Christian D

AU - Young, Clifford

AU - Nielsen, Michael Lund

AU - Olsen, Jesper V

AU - Brakebusch, Cord

AU - Choudhary, Chuna Ram

PY - 2012

Y1 - 2012

N2 - Posttranslational modifications of proteins increase the complexity of the cellular proteome andenable rapid regulation of protein functions in response to environmental changes. Proteinubiquitylation is a central regulatory posttranslational modification that controls numerousbiological processes including proteasomal degradation of proteins, DNA damage repair and innateimmune responses. Here we combine high-resolution mass spectrometry with single-stepimmunoenrichment of di-glycine modified peptides for mapping of endogenous putativeubiquitylation sites in murine tissues. We identify more than 20,000 unique ubiquitylation sites onproteins involved in diverse biological processes. Our data reveals that ubiquitylation regulates coresignaling pathways common for each of the studied tissues. In addition, we discover thatubiquitylation regulates tissue-specific signaling networks. Many tissue-specific ubiquitylation siteswere obtained from brain highlighting the complexity and unique physiology of this organ. Wefurther demonstrate that different di-glycine-lysine-specific monoclonal antibodies exhibit sequencepreferences, and that their complementary use increases the depth of ubiquitylation site analysis,thereby providing a more unbiased view of protein ubiquitylation.

AB - Posttranslational modifications of proteins increase the complexity of the cellular proteome andenable rapid regulation of protein functions in response to environmental changes. Proteinubiquitylation is a central regulatory posttranslational modification that controls numerousbiological processes including proteasomal degradation of proteins, DNA damage repair and innateimmune responses. Here we combine high-resolution mass spectrometry with single-stepimmunoenrichment of di-glycine modified peptides for mapping of endogenous putativeubiquitylation sites in murine tissues. We identify more than 20,000 unique ubiquitylation sites onproteins involved in diverse biological processes. Our data reveals that ubiquitylation regulates coresignaling pathways common for each of the studied tissues. In addition, we discover thatubiquitylation regulates tissue-specific signaling networks. Many tissue-specific ubiquitylation siteswere obtained from brain highlighting the complexity and unique physiology of this organ. Wefurther demonstrate that different di-glycine-lysine-specific monoclonal antibodies exhibit sequencepreferences, and that their complementary use increases the depth of ubiquitylation site analysis,thereby providing a more unbiased view of protein ubiquitylation.

U2 - 10.1074/mcp.M112.017905

DO - 10.1074/mcp.M112.017905

M3 - Journal article

C2 - 22790023

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

SN - 1535-9476

ER -