Dicer-like (DCL) proteins in plants
Dicer and Dicer-like (DCL) proteins are key components in small RNA biogenesis. DCLs form a small protein family in plants whose diversification time dates to the emergence of mosses (Physcomitrella patens). DCLs are ubiquitously but not evenly expressed in tissues, at different developmental stages...
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| Veröffentlicht in: | Functional & integrative genomics 2009-08, Vol.9 (3), p.277-286 |
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| creator | Liu, Qingpo Feng, Ying Zhu, Zhujun |
| description | Dicer and Dicer-like (DCL) proteins are key components in small RNA biogenesis. DCLs form a small protein family in plants whose diversification time dates to the emergence of mosses (Physcomitrella patens). DCLs are ubiquitously but not evenly expressed in tissues, at different developmental stages, and in response to environmental stresses. In Arabidopsis, AtDCL1, AtDCL2, and AtDCL4 exhibit similar expression pattern during the leaf or stem development, which is distinguished from AtDCL3. However, distinct expression profiles for all DCLs are found during the development of reproductive organs flower and seed. The grape VvDCL1 and VvDCL3 may act sequentially to face the fungi challenge. Overall, the responses of DCLs to drought, cold, and salt are quite different, indicating that plants might have specialized regulatory mechanism in response to different abiotic stresses. Further analysis of the promoter regions reveals a few of cis-elements that are hormone- and stress-responsive and developmental-related. However, gain and loss of cis-elements are frequent during evolution, and not only paralogous but also orthologous DCLs have dissimilar cis-element organization. In addition to cis-elements, AtDCL1 is probably regulated by both ath-miR162 and ath-miR414. Posterior analysis has identified some critical amino acid sites that are responsible for functional divergence between DCL family members. These findings provide new insights into understanding DCL protein functions. |
| doi_str_mv | 10.1007/s10142-009-0111-5 |
| format | Article |
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DCLs form a small protein family in plants whose diversification time dates to the emergence of mosses (Physcomitrella patens). DCLs are ubiquitously but not evenly expressed in tissues, at different developmental stages, and in response to environmental stresses. In Arabidopsis, AtDCL1, AtDCL2, and AtDCL4 exhibit similar expression pattern during the leaf or stem development, which is distinguished from AtDCL3. However, distinct expression profiles for all DCLs are found during the development of reproductive organs flower and seed. The grape VvDCL1 and VvDCL3 may act sequentially to face the fungi challenge. Overall, the responses of DCLs to drought, cold, and salt are quite different, indicating that plants might have specialized regulatory mechanism in response to different abiotic stresses. Further analysis of the promoter regions reveals a few of cis-elements that are hormone- and stress-responsive and developmental-related. However, gain and loss of cis-elements are frequent during evolution, and not only paralogous but also orthologous DCLs have dissimilar cis-element organization. In addition to cis-elements, AtDCL1 is probably regulated by both ath-miR162 and ath-miR414. Posterior analysis has identified some critical amino acid sites that are responsible for functional divergence between DCL family members. These findings provide new insights into understanding DCL protein functions.</description><identifier>ISSN: 1438-793X</identifier><identifier>EISSN: 1438-7948</identifier><identifier>DOI: 10.1007/s10142-009-0111-5</identifier><identifier>PMID: 19221817</identifier><language>eng</language><publisher>Berlin/Heidelberg: Berlin/Heidelberg : Springer-Verlag</publisher><subject>Animal Genetics and Genomics ; Animals ; Arabidopsis ; Arabidopsis - physiology ; Biochemistry ; Bioinformatics ; Biological and medical sciences ; Biomedical and Life Sciences ; Cell Biology ; Cis-elements ; Databases, Nucleic Acid ; Dicer-like ; Evolution, Molecular ; Expression ; Functional divergence ; Fundamental and applied biological sciences. Psychology ; Gene expression ; Gene Expression Regulation, Plant ; General aspects ; Life Sciences ; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) ; Microbial Genetics and Genomics ; Phylogeny ; Physcomitrella patens ; Plant ; Plant biology ; Plant Genetics and Genomics ; Plant Proteins - classification ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Proteins ; Review ; Ribonuclease III - classification ; Ribonuclease III - genetics ; Ribonuclease III - metabolism ; Ribonucleic acid ; RNA ; RNA, Untranslated - genetics ; RNA, Untranslated - metabolism ; Stress, Physiological ; Vitaceae</subject><ispartof>Functional & integrative genomics, 2009-08, Vol.9 (3), p.277-286</ispartof><rights>Springer-Verlag 2009</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c454t-f3e625554127ef669ba1d078535e55cf5a956d92a2e3ac43f48d43b84d320dd23</citedby><cites>FETCH-LOGICAL-c454t-f3e625554127ef669ba1d078535e55cf5a956d92a2e3ac43f48d43b84d320dd23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10142-009-0111-5$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10142-009-0111-5$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21658457$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19221817$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Qingpo</creatorcontrib><creatorcontrib>Feng, Ying</creatorcontrib><creatorcontrib>Zhu, Zhujun</creatorcontrib><title>Dicer-like (DCL) proteins in plants</title><title>Functional & integrative genomics</title><addtitle>Funct Integr Genomics</addtitle><addtitle>Funct Integr Genomics</addtitle><description>Dicer and Dicer-like (DCL) proteins are key components in small RNA biogenesis. DCLs form a small protein family in plants whose diversification time dates to the emergence of mosses (Physcomitrella patens). DCLs are ubiquitously but not evenly expressed in tissues, at different developmental stages, and in response to environmental stresses. In Arabidopsis, AtDCL1, AtDCL2, and AtDCL4 exhibit similar expression pattern during the leaf or stem development, which is distinguished from AtDCL3. However, distinct expression profiles for all DCLs are found during the development of reproductive organs flower and seed. The grape VvDCL1 and VvDCL3 may act sequentially to face the fungi challenge. Overall, the responses of DCLs to drought, cold, and salt are quite different, indicating that plants might have specialized regulatory mechanism in response to different abiotic stresses. Further analysis of the promoter regions reveals a few of cis-elements that are hormone- and stress-responsive and developmental-related. However, gain and loss of cis-elements are frequent during evolution, and not only paralogous but also orthologous DCLs have dissimilar cis-element organization. In addition to cis-elements, AtDCL1 is probably regulated by both ath-miR162 and ath-miR414. Posterior analysis has identified some critical amino acid sites that are responsible for functional divergence between DCL family members. These findings provide new insights into understanding DCL protein functions.</description><subject>Animal Genetics and Genomics</subject><subject>Animals</subject><subject>Arabidopsis</subject><subject>Arabidopsis - physiology</subject><subject>Biochemistry</subject><subject>Bioinformatics</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Cell Biology</subject><subject>Cis-elements</subject><subject>Databases, Nucleic Acid</subject><subject>Dicer-like</subject><subject>Evolution, Molecular</subject><subject>Expression</subject><subject>Functional divergence</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant</subject><subject>General aspects</subject><subject>Life Sciences</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</subject><subject>Microbial Genetics and Genomics</subject><subject>Phylogeny</subject><subject>Physcomitrella patens</subject><subject>Plant</subject><subject>Plant biology</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Proteins - classification</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Proteins</subject><subject>Review</subject><subject>Ribonuclease III - classification</subject><subject>Ribonuclease III - genetics</subject><subject>Ribonuclease III - metabolism</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Untranslated - genetics</subject><subject>RNA, Untranslated - metabolism</subject><subject>Stress, Physiological</subject><subject>Vitaceae</subject><issn>1438-793X</issn><issn>1438-7948</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqFkE1LxDAQhoMofv8AL7ooih6qM5NM2xxl_YQFDyp4C9k2lWq3XZPdg__eLF0UPOgpgTzz5p1HiD2EcwTILgICKkoAdAKImPCK2EQl8yTTKl_9vsuXDbEVwhsAMGi5LjZQE2GO2aY4uqoL55OmfneD06vh6Gww9d3M1W0Y1O1g2th2FnbEWmWb4HaX57Z4vrl-Gt4lo4fb--HlKCkUq1lSSZcSMyukzFVpqscWS8hyluyYi4qt5rTUZMlJWyhZqbxUcpyrUhKUJcltcdLnxgofcxdmZlKHwjWxhOvmwaSZwjRD_hekaIQ1QQQPf4Fv3dy3cQlDqLVCJhkh7KHCdyF4V5mpryfWfxoEs_Bses8mppqFZ7NosL8Mno8nrvyZWIqNwPESsKGwTeVtW9ThmyNMOVe84KjnQnxqX53_afjX7wf9UGU7Y199DH5-JEAJmKoYS_ILsI6ZuA</recordid><startdate>20090801</startdate><enddate>20090801</enddate><creator>Liu, Qingpo</creator><creator>Feng, Ying</creator><creator>Zhu, Zhujun</creator><general>Berlin/Heidelberg : Springer-Verlag</general><general>Springer-Verlag</general><general>Springer</general><general>Springer Nature B.V</general><scope>FBQ</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>3V.</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PADUT</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>M7N</scope><scope>7X8</scope></search><sort><creationdate>20090801</creationdate><title>Dicer-like (DCL) proteins in plants</title><author>Liu, Qingpo ; Feng, Ying ; Zhu, Zhujun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c454t-f3e625554127ef669ba1d078535e55cf5a956d92a2e3ac43f48d43b84d320dd23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Animal Genetics and Genomics</topic><topic>Animals</topic><topic>Arabidopsis</topic><topic>Arabidopsis - physiology</topic><topic>Biochemistry</topic><topic>Bioinformatics</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Cell Biology</topic><topic>Cis-elements</topic><topic>Databases, Nucleic Acid</topic><topic>Dicer-like</topic><topic>Evolution, Molecular</topic><topic>Expression</topic><topic>Functional divergence</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Plant</topic><topic>General aspects</topic><topic>Life Sciences</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>Microbial Genetics and Genomics</topic><topic>Phylogeny</topic><topic>Physcomitrella patens</topic><topic>Plant</topic><topic>Plant biology</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Proteins - classification</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Proteins</topic><topic>Review</topic><topic>Ribonuclease III - classification</topic><topic>Ribonuclease III - genetics</topic><topic>Ribonuclease III - metabolism</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA, Untranslated - genetics</topic><topic>RNA, Untranslated - metabolism</topic><topic>Stress, Physiological</topic><topic>Vitaceae</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Qingpo</creatorcontrib><creatorcontrib>Feng, Ying</creatorcontrib><creatorcontrib>Zhu, Zhujun</creatorcontrib><collection>AGRIS</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>ProQuest Central (Corporate)</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Research Library China</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>MEDLINE - Academic</collection><jtitle>Functional & integrative genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Qingpo</au><au>Feng, Ying</au><au>Zhu, Zhujun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dicer-like (DCL) proteins in plants</atitle><jtitle>Functional & integrative genomics</jtitle><stitle>Funct Integr Genomics</stitle><addtitle>Funct Integr Genomics</addtitle><date>2009-08-01</date><risdate>2009</risdate><volume>9</volume><issue>3</issue><spage>277</spage><epage>286</epage><pages>277-286</pages><issn>1438-793X</issn><eissn>1438-7948</eissn><abstract>Dicer and Dicer-like (DCL) proteins are key components in small RNA biogenesis. DCLs form a small protein family in plants whose diversification time dates to the emergence of mosses (Physcomitrella patens). DCLs are ubiquitously but not evenly expressed in tissues, at different developmental stages, and in response to environmental stresses. In Arabidopsis, AtDCL1, AtDCL2, and AtDCL4 exhibit similar expression pattern during the leaf or stem development, which is distinguished from AtDCL3. However, distinct expression profiles for all DCLs are found during the development of reproductive organs flower and seed. The grape VvDCL1 and VvDCL3 may act sequentially to face the fungi challenge. Overall, the responses of DCLs to drought, cold, and salt are quite different, indicating that plants might have specialized regulatory mechanism in response to different abiotic stresses. Further analysis of the promoter regions reveals a few of cis-elements that are hormone- and stress-responsive and developmental-related. However, gain and loss of cis-elements are frequent during evolution, and not only paralogous but also orthologous DCLs have dissimilar cis-element organization. In addition to cis-elements, AtDCL1 is probably regulated by both ath-miR162 and ath-miR414. Posterior analysis has identified some critical amino acid sites that are responsible for functional divergence between DCL family members. These findings provide new insights into understanding DCL protein functions.</abstract><cop>Berlin/Heidelberg</cop><pub>Berlin/Heidelberg : Springer-Verlag</pub><pmid>19221817</pmid><doi>10.1007/s10142-009-0111-5</doi><tpages>10</tpages></addata></record> |
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| subjects | Animal Genetics and Genomics Animals Arabidopsis Arabidopsis - physiology Biochemistry Bioinformatics Biological and medical sciences Biomedical and Life Sciences Cell Biology Cis-elements Databases, Nucleic Acid Dicer-like Evolution, Molecular Expression Functional divergence Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Regulation, Plant General aspects Life Sciences Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Microbial Genetics and Genomics Phylogeny Physcomitrella patens Plant Plant biology Plant Genetics and Genomics Plant Proteins - classification Plant Proteins - genetics Plant Proteins - metabolism Proteins Review Ribonuclease III - classification Ribonuclease III - genetics Ribonuclease III - metabolism Ribonucleic acid RNA RNA, Untranslated - genetics RNA, Untranslated - metabolism Stress, Physiological Vitaceae |
| title | Dicer-like (DCL) proteins in plants |
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