The subcellular proteome of undifferentiated human embryonic stem cells
We have characterized the subcellular proteome of human embryonic stem cells (hESCs) through MS analysis of the membrane, cytosolic, and nuclear fractions, isolated from the same sample of undifferentiated hESCs. Strikingly, 74% of all proteins identified were detected in a single subcellular fracti...
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| Veröffentlicht in: | Proteomics (Weinheim) 2012-02, Vol.12 (3), p.421-430 |
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| creator | Sarkar, Prasenjit Collier, Timothy S. Randall, Shan M. Muddiman, David C. Rao, Balaji M. |
| description | We have characterized the subcellular proteome of human embryonic stem cells (hESCs) through MS analysis of the membrane, cytosolic, and nuclear fractions, isolated from the same sample of undifferentiated hESCs. Strikingly, 74% of all proteins identified were detected in a single subcellular fraction; we also carried out immunofluorescence studies to validate the subcellular localization suggested by proteomic analysis, for a subset of proteins. Our approach resulted in deeper proteome coverage – peptides mapping to 893, 2475, and 1185 proteins were identified in the nuclear, cytosolic, and membrane fractions, respectively. Additionally, we used spectral counting to estimate the relative abundance of all cytosolic proteins. A large number of proteins relevant to hESC biology, including growth factor receptors, cell junction proteins, transcription factors, chromatin remodeling proteins, and histone modifying enzymes were identified. Our analysis shows that components of a large number of interacting signaling pathways are expressed in hESCs. Finally, we show that proteomic analysis of the endoplasmic reticulum (ER) and Golgi compartments is a powerful alternative approach to identify secreted proteins since these are synthesized in the ER and transit through the Golgi. Taken together, our results show that systematic subcellular proteomic analysis is a valuable tool for studying hESC biology. |
| doi_str_mv | 10.1002/pmic.201100507 |
| format | Article |
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Strikingly, 74% of all proteins identified were detected in a single subcellular fraction; we also carried out immunofluorescence studies to validate the subcellular localization suggested by proteomic analysis, for a subset of proteins. Our approach resulted in deeper proteome coverage – peptides mapping to 893, 2475, and 1185 proteins were identified in the nuclear, cytosolic, and membrane fractions, respectively. Additionally, we used spectral counting to estimate the relative abundance of all cytosolic proteins. A large number of proteins relevant to hESC biology, including growth factor receptors, cell junction proteins, transcription factors, chromatin remodeling proteins, and histone modifying enzymes were identified. Our analysis shows that components of a large number of interacting signaling pathways are expressed in hESCs. Finally, we show that proteomic analysis of the endoplasmic reticulum (ER) and Golgi compartments is a powerful alternative approach to identify secreted proteins since these are synthesized in the ER and transit through the Golgi. Taken together, our results show that systematic subcellular proteomic analysis is a valuable tool for studying hESC biology.</description><identifier>ISSN: 1615-9853</identifier><identifier>EISSN: 1615-9861</identifier><identifier>DOI: 10.1002/pmic.201100507</identifier><identifier>PMID: 22144211</identifier><language>eng</language><publisher>Weinheim: WILEY-VCH Verlag</publisher><subject>Analytical, structural and metabolic biochemistry ; Animals ; Biological and medical sciences ; Cell biology ; Cell Differentiation ; Cells, Cultured ; Culture Media, Conditioned ; Cytosol - metabolism ; Embryonic Stem Cells - cytology ; Embryonic Stem Cells - metabolism ; Endoplasmic Reticulum - genetics ; Endoplasmic Reticulum - metabolism ; Extracellular proteins ; Fundamental and applied biological sciences. Psychology ; Gene Expression Regulation, Developmental ; Golgi Apparatus - genetics ; Golgi Apparatus - metabolism ; Human embryonic stem cells ; Humans ; Medical research ; Membrane Proteins - genetics ; Membrane Proteins - metabolism ; Mice ; Miscellaneous ; Nuclear Proteins - genetics ; Nuclear Proteins - metabolism ; Proteins ; Signal Transduction - genetics ; Stem cells ; Subcellular fractionation ; Subcellular Fractions - metabolism ; Subcellular proteomics</subject><ispartof>Proteomics (Weinheim), 2012-02, Vol.12 (3), p.421-430</ispartof><rights>Copyright © 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.</rights><rights>Copyright © 2012 WILEY-VCH Verlag GmbH & Co. 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Strikingly, 74% of all proteins identified were detected in a single subcellular fraction; we also carried out immunofluorescence studies to validate the subcellular localization suggested by proteomic analysis, for a subset of proteins. Our approach resulted in deeper proteome coverage – peptides mapping to 893, 2475, and 1185 proteins were identified in the nuclear, cytosolic, and membrane fractions, respectively. Additionally, we used spectral counting to estimate the relative abundance of all cytosolic proteins. A large number of proteins relevant to hESC biology, including growth factor receptors, cell junction proteins, transcription factors, chromatin remodeling proteins, and histone modifying enzymes were identified. Our analysis shows that components of a large number of interacting signaling pathways are expressed in hESCs. Finally, we show that proteomic analysis of the endoplasmic reticulum (ER) and Golgi compartments is a powerful alternative approach to identify secreted proteins since these are synthesized in the ER and transit through the Golgi. Taken together, our results show that systematic subcellular proteomic analysis is a valuable tool for studying hESC biology.</description><subject>Analytical, structural and metabolic biochemistry</subject><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Cell biology</subject><subject>Cell Differentiation</subject><subject>Cells, Cultured</subject><subject>Culture Media, Conditioned</subject><subject>Cytosol - metabolism</subject><subject>Embryonic Stem Cells - cytology</subject><subject>Embryonic Stem Cells - metabolism</subject><subject>Endoplasmic Reticulum - genetics</subject><subject>Endoplasmic Reticulum - metabolism</subject><subject>Extracellular proteins</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Golgi Apparatus - genetics</subject><subject>Golgi Apparatus - metabolism</subject><subject>Human embryonic stem cells</subject><subject>Humans</subject><subject>Medical research</subject><subject>Membrane Proteins - genetics</subject><subject>Membrane Proteins - metabolism</subject><subject>Mice</subject><subject>Miscellaneous</subject><subject>Nuclear Proteins - genetics</subject><subject>Nuclear Proteins - metabolism</subject><subject>Proteins</subject><subject>Signal Transduction - genetics</subject><subject>Stem cells</subject><subject>Subcellular fractionation</subject><subject>Subcellular Fractions - metabolism</subject><subject>Subcellular proteomics</subject><issn>1615-9853</issn><issn>1615-9861</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUtv1DAUhSMEog_YskSRUEU3GXwdO46XaFSGVuUhMRR2lmNfqy55DHaiMv8eRzMMiAWsbEvfuT7nnix7BmQBhNBXm86bBSWQHpyIB9kxVMALWVfw8HDn5VF2EuMdISBqKR5nR5QCYxTgOFutbzGPU2OwbadWh3wThhGHDvPB5VNvvXMYsB-9HtHmt1On-xy7JmyH3ps8jtjlszQ-yR453UZ8uj9Ps89vLtbLt8X1h9Xl8vV1YXgpRSGcNsYybSi6hrHKaSgpo9wCsUwKRljDjWtq7rhFrCuNRtS8AllbYlFCeZq93M1NPr9PGEfV-Tg70D0OU1QSJKVzykSe_5METqXknNUz-uIv9G6YQp9yJAoEY5xXNFGLHWXCEGNApzbBdzpsFRA1l6HmMtShjCR4vh87NR3aA_5r-wk42wM6Gt26oHvj42-OVyWkJImTO-7et7j9z7fq47vL5Z8mip3Wp7J-HLQ6fFOVKAVXX96v1Ff-6ebqZr1UovwJp5ixzw</recordid><startdate>201202</startdate><enddate>201202</enddate><creator>Sarkar, Prasenjit</creator><creator>Collier, Timothy S.</creator><creator>Randall, Shan M.</creator><creator>Muddiman, David C.</creator><creator>Rao, Balaji M.</creator><general>WILEY-VCH Verlag</general><general>WILEY‐VCH Verlag</general><general>Wiley-VCH</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201202</creationdate><title>The subcellular proteome of undifferentiated human embryonic stem cells</title><author>Sarkar, Prasenjit ; Collier, Timothy S. ; Randall, Shan M. ; Muddiman, David C. ; Rao, Balaji M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5397-7faccd4ac2efb446fa132425d10d497404b5cfb85f5dee86aec7856198d0de913</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Analytical, structural and metabolic biochemistry</topic><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>Cell biology</topic><topic>Cell Differentiation</topic><topic>Cells, Cultured</topic><topic>Culture Media, Conditioned</topic><topic>Cytosol - metabolism</topic><topic>Embryonic Stem Cells - cytology</topic><topic>Embryonic Stem Cells - metabolism</topic><topic>Endoplasmic Reticulum - genetics</topic><topic>Endoplasmic Reticulum - metabolism</topic><topic>Extracellular proteins</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Regulation, Developmental</topic><topic>Golgi Apparatus - genetics</topic><topic>Golgi Apparatus - metabolism</topic><topic>Human embryonic stem cells</topic><topic>Humans</topic><topic>Medical research</topic><topic>Membrane Proteins - genetics</topic><topic>Membrane Proteins - metabolism</topic><topic>Mice</topic><topic>Miscellaneous</topic><topic>Nuclear Proteins - genetics</topic><topic>Nuclear Proteins - metabolism</topic><topic>Proteins</topic><topic>Signal Transduction - genetics</topic><topic>Stem cells</topic><topic>Subcellular fractionation</topic><topic>Subcellular Fractions - metabolism</topic><topic>Subcellular proteomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sarkar, Prasenjit</creatorcontrib><creatorcontrib>Collier, Timothy S.</creatorcontrib><creatorcontrib>Randall, Shan M.</creatorcontrib><creatorcontrib>Muddiman, David C.</creatorcontrib><creatorcontrib>Rao, Balaji M.</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Proteomics (Weinheim)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sarkar, Prasenjit</au><au>Collier, Timothy S.</au><au>Randall, Shan M.</au><au>Muddiman, David C.</au><au>Rao, Balaji M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The subcellular proteome of undifferentiated human embryonic stem cells</atitle><jtitle>Proteomics (Weinheim)</jtitle><addtitle>Proteomics</addtitle><date>2012-02</date><risdate>2012</risdate><volume>12</volume><issue>3</issue><spage>421</spage><epage>430</epage><pages>421-430</pages><issn>1615-9853</issn><eissn>1615-9861</eissn><abstract>We have characterized the subcellular proteome of human embryonic stem cells (hESCs) through MS analysis of the membrane, cytosolic, and nuclear fractions, isolated from the same sample of undifferentiated hESCs. Strikingly, 74% of all proteins identified were detected in a single subcellular fraction; we also carried out immunofluorescence studies to validate the subcellular localization suggested by proteomic analysis, for a subset of proteins. Our approach resulted in deeper proteome coverage – peptides mapping to 893, 2475, and 1185 proteins were identified in the nuclear, cytosolic, and membrane fractions, respectively. Additionally, we used spectral counting to estimate the relative abundance of all cytosolic proteins. A large number of proteins relevant to hESC biology, including growth factor receptors, cell junction proteins, transcription factors, chromatin remodeling proteins, and histone modifying enzymes were identified. Our analysis shows that components of a large number of interacting signaling pathways are expressed in hESCs. Finally, we show that proteomic analysis of the endoplasmic reticulum (ER) and Golgi compartments is a powerful alternative approach to identify secreted proteins since these are synthesized in the ER and transit through the Golgi. Taken together, our results show that systematic subcellular proteomic analysis is a valuable tool for studying hESC biology.</abstract><cop>Weinheim</cop><pub>WILEY-VCH Verlag</pub><pmid>22144211</pmid><doi>10.1002/pmic.201100507</doi><tpages>10</tpages></addata></record> |
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| subjects | Analytical, structural and metabolic biochemistry Animals Biological and medical sciences Cell biology Cell Differentiation Cells, Cultured Culture Media, Conditioned Cytosol - metabolism Embryonic Stem Cells - cytology Embryonic Stem Cells - metabolism Endoplasmic Reticulum - genetics Endoplasmic Reticulum - metabolism Extracellular proteins Fundamental and applied biological sciences. Psychology Gene Expression Regulation, Developmental Golgi Apparatus - genetics Golgi Apparatus - metabolism Human embryonic stem cells Humans Medical research Membrane Proteins - genetics Membrane Proteins - metabolism Mice Miscellaneous Nuclear Proteins - genetics Nuclear Proteins - metabolism Proteins Signal Transduction - genetics Stem cells Subcellular fractionation Subcellular Fractions - metabolism Subcellular proteomics |
| title | The subcellular proteome of undifferentiated human embryonic stem cells |
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