Evolution of Drosophila ribosomal protein gene core promoters
The coordinated expression of ribosomal protein genes (RPGs) has been well documented in many species. Previous analyses of RPG promoters focus only on Fungi and mammals. Recognizing this gap and using a comparative genomics approach, we utilize a motif-finding algorithm that incorporates cross-spec...
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| Veröffentlicht in: | Gene 2009-03, Vol.432 (1), p.54-59 |
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| creator | Ma, Xiaotu Zhang, Kangyu Li, Xiaoman |
| description | The coordinated expression of ribosomal protein genes (RPGs) has been well documented in many species. Previous analyses of RPG promoters focus only on Fungi and mammals. Recognizing this gap and using a comparative genomics approach, we utilize a motif-finding algorithm that incorporates cross-species conservation to identify several significant motifs in
Drosophila RPG promoters. As a result, significant differences of the enriched motifs in RPG promoter are found among
Drosophila, Fungi, and mammals, demonstrating the evolutionary dynamics of the ribosomal gene regulatory network. We also report a motif present in similar numbers of RPGs among
Drosophila species which does not appear to be conserved at the individual RPG gene level. A module-wise stabilizing selection theory is proposed to explain this observation. Overall, our results provide significant insight into the fast-evolving nature of transcriptional regulation in the RPG module. |
| doi_str_mv | 10.1016/j.gene.2008.10.025 |
| format | Article |
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Drosophila RPG promoters. As a result, significant differences of the enriched motifs in RPG promoter are found among
Drosophila, Fungi, and mammals, demonstrating the evolutionary dynamics of the ribosomal gene regulatory network. We also report a motif present in similar numbers of RPGs among
Drosophila species which does not appear to be conserved at the individual RPG gene level. A module-wise stabilizing selection theory is proposed to explain this observation. Overall, our results provide significant insight into the fast-evolving nature of transcriptional regulation in the RPG module.</description><identifier>ISSN: 0378-1119</identifier><identifier>EISSN: 1879-0038</identifier><identifier>DOI: 10.1016/j.gene.2008.10.025</identifier><identifier>PMID: 19059316</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Amino Acid Sequence ; Animals ; Base Sequence ; Codon - genetics ; Conserved Sequence ; DNA Replication - genetics ; Drosophila ; Drosophila - genetics ; Drosophila Proteins - genetics ; Evolution ; Evolution, Molecular ; Fungi - genetics ; Genes, Insect ; Mammals - genetics ; Molecular Sequence Data ; Motif ; Promoter ; Promoter Regions, Genetic ; Protein Biosynthesis ; Protein Structure, Tertiary ; Ribosomal protein ; Ribosomal Proteins - genetics ; Selection, Genetic ; Species Specificity ; Transcription Factors - chemistry</subject><ispartof>Gene, 2009-03, Vol.432 (1), p.54-59</ispartof><rights>2008 Elsevier B.V.</rights><rights>2008 Elsevier B.V. All rights reserved. 2008</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c550t-1e725002c6a4e087e585eb39b9b12168a9bcfa67a25c61e1f28c363577c1e9143</citedby><cites>FETCH-LOGICAL-c550t-1e725002c6a4e087e585eb39b9b12168a9bcfa67a25c61e1f28c363577c1e9143</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0378111908005635$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,776,780,881,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19059316$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ma, Xiaotu</creatorcontrib><creatorcontrib>Zhang, Kangyu</creatorcontrib><creatorcontrib>Li, Xiaoman</creatorcontrib><title>Evolution of Drosophila ribosomal protein gene core promoters</title><title>Gene</title><addtitle>Gene</addtitle><description>The coordinated expression of ribosomal protein genes (RPGs) has been well documented in many species. Previous analyses of RPG promoters focus only on Fungi and mammals. Recognizing this gap and using a comparative genomics approach, we utilize a motif-finding algorithm that incorporates cross-species conservation to identify several significant motifs in
Drosophila RPG promoters. As a result, significant differences of the enriched motifs in RPG promoter are found among
Drosophila, Fungi, and mammals, demonstrating the evolutionary dynamics of the ribosomal gene regulatory network. We also report a motif present in similar numbers of RPGs among
Drosophila species which does not appear to be conserved at the individual RPG gene level. A module-wise stabilizing selection theory is proposed to explain this observation. Overall, our results provide significant insight into the fast-evolving nature of transcriptional regulation in the RPG module.</description><subject>Amino Acid Sequence</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>Codon - genetics</subject><subject>Conserved Sequence</subject><subject>DNA Replication - genetics</subject><subject>Drosophila</subject><subject>Drosophila - genetics</subject><subject>Drosophila Proteins - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Fungi - genetics</subject><subject>Genes, Insect</subject><subject>Mammals - genetics</subject><subject>Molecular Sequence Data</subject><subject>Motif</subject><subject>Promoter</subject><subject>Promoter Regions, Genetic</subject><subject>Protein Biosynthesis</subject><subject>Protein Structure, Tertiary</subject><subject>Ribosomal protein</subject><subject>Ribosomal Proteins - genetics</subject><subject>Selection, Genetic</subject><subject>Species Specificity</subject><subject>Transcription Factors - chemistry</subject><issn>0378-1119</issn><issn>1879-0038</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUU1P3DAQtRAVbBf-AAeUE7dsZ-y140gFqaL0Q0LqpZwtxzsBr5J4sbMr9d_X0a4oXKgvY7158zx-j7ELhAUCqk_rxSMNtOAAOgML4PKIzVBXdQkg9DGbgah0iYj1KfuY0hrykZKfsFOsQdYC1Yxd3-1Ctx19GIrQFl9jSGHz5DtbRN_ke2-7YhPDSH4opscKFyJNSJ-xmM7Yh9Z2ic4Pdc4evt39vv1R3v_6_vP2y33ppISxRKq4BOBO2SWBrkhqSY2om7pBjkrbunGtVZXl0ikkbLl2QglZVQ6pxqWYs5u97mbb9LRyNIzRdmYTfW_jHxOsN287g38yj2FnBBcc1CRwdRCI4XlLaTS9T466zg4Utskopaul1Py_RA5cL3lebs74nuiyZylS-7INgpniMWszOWameCYsx5OHLl__49_IIY9M-LwnUHZz5yma5DwNjlY-khvNKvj39P8Cf3Shog</recordid><startdate>20090301</startdate><enddate>20090301</enddate><creator>Ma, Xiaotu</creator><creator>Zhang, Kangyu</creator><creator>Li, Xiaoman</creator><general>Elsevier B.V</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>7SS</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20090301</creationdate><title>Evolution of Drosophila ribosomal protein gene core promoters</title><author>Ma, Xiaotu ; Zhang, Kangyu ; Li, Xiaoman</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c550t-1e725002c6a4e087e585eb39b9b12168a9bcfa67a25c61e1f28c363577c1e9143</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Amino Acid Sequence</topic><topic>Animals</topic><topic>Base Sequence</topic><topic>Codon - genetics</topic><topic>Conserved Sequence</topic><topic>DNA Replication - genetics</topic><topic>Drosophila</topic><topic>Drosophila - genetics</topic><topic>Drosophila Proteins - genetics</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Fungi - genetics</topic><topic>Genes, Insect</topic><topic>Mammals - genetics</topic><topic>Molecular Sequence Data</topic><topic>Motif</topic><topic>Promoter</topic><topic>Promoter Regions, Genetic</topic><topic>Protein Biosynthesis</topic><topic>Protein Structure, Tertiary</topic><topic>Ribosomal protein</topic><topic>Ribosomal Proteins - genetics</topic><topic>Selection, Genetic</topic><topic>Species Specificity</topic><topic>Transcription Factors - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ma, Xiaotu</creatorcontrib><creatorcontrib>Zhang, Kangyu</creatorcontrib><creatorcontrib>Li, Xiaoman</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Gene</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ma, Xiaotu</au><au>Zhang, Kangyu</au><au>Li, Xiaoman</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evolution of Drosophila ribosomal protein gene core promoters</atitle><jtitle>Gene</jtitle><addtitle>Gene</addtitle><date>2009-03-01</date><risdate>2009</risdate><volume>432</volume><issue>1</issue><spage>54</spage><epage>59</epage><pages>54-59</pages><issn>0378-1119</issn><eissn>1879-0038</eissn><abstract>The coordinated expression of ribosomal protein genes (RPGs) has been well documented in many species. Previous analyses of RPG promoters focus only on Fungi and mammals. Recognizing this gap and using a comparative genomics approach, we utilize a motif-finding algorithm that incorporates cross-species conservation to identify several significant motifs in
Drosophila RPG promoters. As a result, significant differences of the enriched motifs in RPG promoter are found among
Drosophila, Fungi, and mammals, demonstrating the evolutionary dynamics of the ribosomal gene regulatory network. We also report a motif present in similar numbers of RPGs among
Drosophila species which does not appear to be conserved at the individual RPG gene level. A module-wise stabilizing selection theory is proposed to explain this observation. Overall, our results provide significant insight into the fast-evolving nature of transcriptional regulation in the RPG module.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>19059316</pmid><doi>10.1016/j.gene.2008.10.025</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Gene, 2009-03, Vol.432 (1), p.54-59 |
| issn | 0378-1119 1879-0038 |
| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Amino Acid Sequence Animals Base Sequence Codon - genetics Conserved Sequence DNA Replication - genetics Drosophila Drosophila - genetics Drosophila Proteins - genetics Evolution Evolution, Molecular Fungi - genetics Genes, Insect Mammals - genetics Molecular Sequence Data Motif Promoter Promoter Regions, Genetic Protein Biosynthesis Protein Structure, Tertiary Ribosomal protein Ribosomal Proteins - genetics Selection, Genetic Species Specificity Transcription Factors - chemistry |
| title | Evolution of Drosophila ribosomal protein gene core promoters |
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