Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome
AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine protein kinase that is activated by cellular perturbations associated with ATP depletion or stress. While AMPK modulates the activity of a variety of targets containing a specific phosphorylation consensus sequence, the number...
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| Veröffentlicht in: | BMC systems biology 2015-03, Vol.9 (1), p.13-13, Article 13 |
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| creator | Marin, Traci L Gongol, Brendan Martin, Marcy King, Stephanie J Smith, Lemar Johnson, David A Subramaniam, Shankar Chien, Shu Shyy, John Y-J |
| description | AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine protein kinase that is activated by cellular perturbations associated with ATP depletion or stress. While AMPK modulates the activity of a variety of targets containing a specific phosphorylation consensus sequence, the number of AMPK targets and their influence over cellular processes is currently thought to be limited.
We queried the human and the mouse proteomes for proteins containing AMPK phosphorylation consensus sequences. Integration of this database into Gaggle software facilitated the construction of probable AMPK-regulated networks based on known and predicted molecular associations. In vitro kinase assays were conducted for preliminary validation of 12 novel AMPK targets across a variety of cellular functional categories, including transcription, translation, cell migration, protein transport, and energy homeostasis. Following initial validation, pathways that include NAD synthetase 1 (NADSYN1) and protein kinase B (AKT2) were hypothesized and experimentally tested to provide a mechanistic basis for AMPK regulation of cell migration and maintenance of cellular NAD(+) concentrations during catabolic processes.
This study delineates an approach that encompasses both in silico procedures and in vitro experiments to produce testable hypotheses for AMPK regulation of cellular processes. |
| doi_str_mv | 10.1186/s12918-015-0156-0 |
| format | Article |
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We queried the human and the mouse proteomes for proteins containing AMPK phosphorylation consensus sequences. Integration of this database into Gaggle software facilitated the construction of probable AMPK-regulated networks based on known and predicted molecular associations. In vitro kinase assays were conducted for preliminary validation of 12 novel AMPK targets across a variety of cellular functional categories, including transcription, translation, cell migration, protein transport, and energy homeostasis. Following initial validation, pathways that include NAD synthetase 1 (NADSYN1) and protein kinase B (AKT2) were hypothesized and experimentally tested to provide a mechanistic basis for AMPK regulation of cell migration and maintenance of cellular NAD(+) concentrations during catabolic processes.
This study delineates an approach that encompasses both in silico procedures and in vitro experiments to produce testable hypotheses for AMPK regulation of cellular processes.</description><identifier>ISSN: 1752-0509</identifier><identifier>EISSN: 1752-0509</identifier><identifier>DOI: 10.1186/s12918-015-0156-0</identifier><identifier>PMID: 25890336</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>AMP-Activated Protein Kinases - metabolism ; Analysis ; Animals ; Biological Transport ; Calcium - metabolism ; Cell Cycle ; Chromatin - metabolism ; Circadian Rhythm ; Consensus Sequence ; Endoplasmic Reticulum Stress ; Enzyme Activation ; Epigenesis, Genetic ; Glucose - metabolism ; Homeostasis ; Humans ; Insulin - metabolism ; Ligases ; Mice ; Organelle Biogenesis ; Phosphorylation ; Protein Binding ; Protein Folding ; Protein kinases ; Proteomics ; Ribosomes - metabolism ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Signal Transduction ; Software ; Systems Biology ; Transcriptional Activation</subject><ispartof>BMC systems biology, 2015-03, Vol.9 (1), p.13-13, Article 13</ispartof><rights>COPYRIGHT 2015 BioMed Central Ltd.</rights><rights>Marin et al.; licensee BioMed Central. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b561t-785cbb9cab8f39a3e9bd1396285723cb2ca62f989ec78a4b021321451c22ea603</citedby><cites>FETCH-LOGICAL-b561t-785cbb9cab8f39a3e9bd1396285723cb2ca62f989ec78a4b021321451c22ea603</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357066/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357066/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,24801,27924,27925,53791,53793,75738,75739</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25890336$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Marin, Traci L</creatorcontrib><creatorcontrib>Gongol, Brendan</creatorcontrib><creatorcontrib>Martin, Marcy</creatorcontrib><creatorcontrib>King, Stephanie J</creatorcontrib><creatorcontrib>Smith, Lemar</creatorcontrib><creatorcontrib>Johnson, David A</creatorcontrib><creatorcontrib>Subramaniam, Shankar</creatorcontrib><creatorcontrib>Chien, Shu</creatorcontrib><creatorcontrib>Shyy, John Y-J</creatorcontrib><title>Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome</title><title>BMC systems biology</title><addtitle>BMC Syst Biol</addtitle><description>AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine protein kinase that is activated by cellular perturbations associated with ATP depletion or stress. While AMPK modulates the activity of a variety of targets containing a specific phosphorylation consensus sequence, the number of AMPK targets and their influence over cellular processes is currently thought to be limited.
We queried the human and the mouse proteomes for proteins containing AMPK phosphorylation consensus sequences. Integration of this database into Gaggle software facilitated the construction of probable AMPK-regulated networks based on known and predicted molecular associations. In vitro kinase assays were conducted for preliminary validation of 12 novel AMPK targets across a variety of cellular functional categories, including transcription, translation, cell migration, protein transport, and energy homeostasis. Following initial validation, pathways that include NAD synthetase 1 (NADSYN1) and protein kinase B (AKT2) were hypothesized and experimentally tested to provide a mechanistic basis for AMPK regulation of cell migration and maintenance of cellular NAD(+) concentrations during catabolic processes.
This study delineates an approach that encompasses both in silico procedures and in vitro experiments to produce testable hypotheses for AMPK regulation of cellular processes.</description><subject>AMP-Activated Protein Kinases - metabolism</subject><subject>Analysis</subject><subject>Animals</subject><subject>Biological Transport</subject><subject>Calcium - metabolism</subject><subject>Cell Cycle</subject><subject>Chromatin - metabolism</subject><subject>Circadian Rhythm</subject><subject>Consensus Sequence</subject><subject>Endoplasmic Reticulum Stress</subject><subject>Enzyme Activation</subject><subject>Epigenesis, Genetic</subject><subject>Glucose - metabolism</subject><subject>Homeostasis</subject><subject>Humans</subject><subject>Insulin - metabolism</subject><subject>Ligases</subject><subject>Mice</subject><subject>Organelle Biogenesis</subject><subject>Phosphorylation</subject><subject>Protein Binding</subject><subject>Protein Folding</subject><subject>Protein kinases</subject><subject>Proteomics</subject><subject>Ribosomes - metabolism</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Signal Transduction</subject><subject>Software</subject><subject>Systems Biology</subject><subject>Transcriptional Activation</subject><issn>1752-0509</issn><issn>1752-0509</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kluL1TAQx4so7kU_gC9S8MV96JpLk7YvwmG9HVhRvDyHSTo9J9omZ5t0cb-9KV2XLayEIUPmN3_mkix7Qck5pbV8EyhraF0QKmaTBXmUHdNKsIII0jy-5x9lJyH8IkRwxqqn2RETdUM4l8cZblt00XbWQLTe5b7LN5-_FmCivYaIbX4YfUTr8t_WQcA8wrjDGHJ9k0NuvAvowhTygFcTOoPJgdHsZ5m4xyXZD_gse9JBH_D57X2a_fzw_sfFp-Lyy8ftxeay0ELSWFS1MFo3BnTd8QY4NrqlvJGsFhXjRjMDknVN3aCpaig1YZQzWgpqGEOQhJ9mbxfdw6QHbE1qbYReHUY7wHijPFi1jji7Vzt_rUouKiJlEni3CGjr_yOwjhg_qGUNKq1gNqnmOl7f1jH6NJgQ1WCDwb4Hh34KisqqlLUkTCT01YLuoEdlXeeTrplxtRElLRNZskSdP0Cl0-Jg0xqws-l9lXC2SkhMxD9xB1MIavv925qlC2tGH8KI3V2_lKj5oz3Y4cv7k77L-Pez-F_r385o</recordid><startdate>20150311</startdate><enddate>20150311</enddate><creator>Marin, Traci L</creator><creator>Gongol, Brendan</creator><creator>Martin, Marcy</creator><creator>King, Stephanie J</creator><creator>Smith, Lemar</creator><creator>Johnson, David A</creator><creator>Subramaniam, Shankar</creator><creator>Chien, Shu</creator><creator>Shyy, John Y-J</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><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>ISR</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150311</creationdate><title>Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome</title><author>Marin, Traci L ; Gongol, Brendan ; Martin, Marcy ; King, Stephanie J ; Smith, Lemar ; Johnson, David A ; Subramaniam, Shankar ; Chien, Shu ; Shyy, John Y-J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b561t-785cbb9cab8f39a3e9bd1396285723cb2ca62f989ec78a4b021321451c22ea603</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>AMP-Activated Protein Kinases - metabolism</topic><topic>Analysis</topic><topic>Animals</topic><topic>Biological Transport</topic><topic>Calcium - metabolism</topic><topic>Cell Cycle</topic><topic>Chromatin - metabolism</topic><topic>Circadian Rhythm</topic><topic>Consensus Sequence</topic><topic>Endoplasmic Reticulum Stress</topic><topic>Enzyme Activation</topic><topic>Epigenesis, Genetic</topic><topic>Glucose - metabolism</topic><topic>Homeostasis</topic><topic>Humans</topic><topic>Insulin - metabolism</topic><topic>Ligases</topic><topic>Mice</topic><topic>Organelle Biogenesis</topic><topic>Phosphorylation</topic><topic>Protein Binding</topic><topic>Protein Folding</topic><topic>Protein kinases</topic><topic>Proteomics</topic><topic>Ribosomes - metabolism</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>Signal Transduction</topic><topic>Software</topic><topic>Systems Biology</topic><topic>Transcriptional Activation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Marin, Traci L</creatorcontrib><creatorcontrib>Gongol, Brendan</creatorcontrib><creatorcontrib>Martin, Marcy</creatorcontrib><creatorcontrib>King, Stephanie J</creatorcontrib><creatorcontrib>Smith, Lemar</creatorcontrib><creatorcontrib>Johnson, David A</creatorcontrib><creatorcontrib>Subramaniam, Shankar</creatorcontrib><creatorcontrib>Chien, Shu</creatorcontrib><creatorcontrib>Shyy, John Y-J</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC systems biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Marin, Traci L</au><au>Gongol, Brendan</au><au>Martin, Marcy</au><au>King, Stephanie J</au><au>Smith, Lemar</au><au>Johnson, David A</au><au>Subramaniam, Shankar</au><au>Chien, Shu</au><au>Shyy, John Y-J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome</atitle><jtitle>BMC systems biology</jtitle><addtitle>BMC Syst Biol</addtitle><date>2015-03-11</date><risdate>2015</risdate><volume>9</volume><issue>1</issue><spage>13</spage><epage>13</epage><pages>13-13</pages><artnum>13</artnum><issn>1752-0509</issn><eissn>1752-0509</eissn><abstract>AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine protein kinase that is activated by cellular perturbations associated with ATP depletion or stress. While AMPK modulates the activity of a variety of targets containing a specific phosphorylation consensus sequence, the number of AMPK targets and their influence over cellular processes is currently thought to be limited.
We queried the human and the mouse proteomes for proteins containing AMPK phosphorylation consensus sequences. Integration of this database into Gaggle software facilitated the construction of probable AMPK-regulated networks based on known and predicted molecular associations. In vitro kinase assays were conducted for preliminary validation of 12 novel AMPK targets across a variety of cellular functional categories, including transcription, translation, cell migration, protein transport, and energy homeostasis. Following initial validation, pathways that include NAD synthetase 1 (NADSYN1) and protein kinase B (AKT2) were hypothesized and experimentally tested to provide a mechanistic basis for AMPK regulation of cell migration and maintenance of cellular NAD(+) concentrations during catabolic processes.
This study delineates an approach that encompasses both in silico procedures and in vitro experiments to produce testable hypotheses for AMPK regulation of cellular processes.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25890336</pmid><doi>10.1186/s12918-015-0156-0</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | AMP-Activated Protein Kinases - metabolism Analysis Animals Biological Transport Calcium - metabolism Cell Cycle Chromatin - metabolism Circadian Rhythm Consensus Sequence Endoplasmic Reticulum Stress Enzyme Activation Epigenesis, Genetic Glucose - metabolism Homeostasis Humans Insulin - metabolism Ligases Mice Organelle Biogenesis Phosphorylation Protein Binding Protein Folding Protein kinases Proteomics Ribosomes - metabolism RNA, Messenger - genetics RNA, Messenger - metabolism Signal Transduction Software Systems Biology Transcriptional Activation |
| title | Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome |
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