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Homeodomain Leucine Zipper Class I Genes in Arabidopsis. Expression Patterns and Phylogenetic Relationships
Members of the homeodomain leucine zipper (HDZip) family of transcription factors are present in a wide range of plants, from mosses to higher plants, but not in other eukaryotes. The HDZip genes act in developmental processes, including vascular tissue and trichome development, and several of them...
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Published in: | Plant physiology (Bethesda) 2005-09, Vol.139 (1), p.509-518 |
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description | Members of the homeodomain leucine zipper (HDZip) family of transcription factors are present in a wide range of plants, from mosses to higher plants, but not in other eukaryotes. The HDZip genes act in developmental processes, including vascular tissue and trichome development, and several of them have been suggested to be involved in the mediation of external signals to regulate plant growth. The Arabidopsis (Arabidopsis thaliana) genome contains 47 HDZip genes, which, based on sequence criteria, have been grouped into four different classes: HDZip I to IV. In this article, we present an overview of the class I HDZip genes in Arabidopsis. We describe their expression patterns, transcriptional regulation properties, duplication history, and phylogeny. The phylogeny of HDZip class I genes is supported by data on the duplication history of the genes, as well as the intron/exon patterning of the HDZip-encoding motifs. The HDZip class I genes were found to be widely expressed and partly to have overlapping expression patterns at the organ level. Further, abscisic acid or water deficit treatments and different light conditions affected the transcript levels of a majority of the HDZip I genes. Within the gene family, our data show examples of closely related HDZip genes with similarities in the function of the gene product, but a divergence in expression pattern. In addition, six HDZip class I proteins tested were found to be activators of gene expression. In conclusion, several HDZip I genes appear to regulate similar cellular processes, although in different organs or tissues and in response to different environmental signals. |
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Expression Patterns and Phylogenetic Relationships</title><source>JSTOR Archival Journals and Primary Sources Collection</source><source>Oxford Journals Online</source><creator>Henriksson, Eva ; Olsson, Anna S.B ; Johannesson, Henrik ; Johansson, Henrik ; Hanson, Johannes ; Engström, Peter ; Söderman, Eva</creator><creatorcontrib>Henriksson, Eva ; Olsson, Anna S.B ; Johannesson, Henrik ; Johansson, Henrik ; Hanson, Johannes ; Engström, Peter ; Söderman, Eva</creatorcontrib><description>Members of the homeodomain leucine zipper (HDZip) family of transcription factors are present in a wide range of plants, from mosses to higher plants, but not in other eukaryotes. The HDZip genes act in developmental processes, including vascular tissue and trichome development, and several of them have been suggested to be involved in the mediation of external signals to regulate plant growth. The Arabidopsis (Arabidopsis thaliana) genome contains 47 HDZip genes, which, based on sequence criteria, have been grouped into four different classes: HDZip I to IV. In this article, we present an overview of the class I HDZip genes in Arabidopsis. We describe their expression patterns, transcriptional regulation properties, duplication history, and phylogeny. The phylogeny of HDZip class I genes is supported by data on the duplication history of the genes, as well as the intron/exon patterning of the HDZip-encoding motifs. The HDZip class I genes were found to be widely expressed and partly to have overlapping expression patterns at the organ level. Further, abscisic acid or water deficit treatments and different light conditions affected the transcript levels of a majority of the HDZip I genes. Within the gene family, our data show examples of closely related HDZip genes with similarities in the function of the gene product, but a divergence in expression pattern. In addition, six HDZip class I proteins tested were found to be activators of gene expression. In conclusion, several HDZip I genes appear to regulate similar cellular processes, although in different organs or tissues and in response to different environmental signals.</description><identifier>ISSN: 0032-0889</identifier><identifier>ISSN: 1532-2548</identifier><identifier>EISSN: 1532-2548</identifier><identifier>DOI: 10.1104/pp.105.063461</identifier><identifier>PMID: 16055682</identifier><identifier>CODEN: PPHYA5</identifier><language>eng</language><publisher>Rockville, MD: American Society of Plant Biologists</publisher><subject>abscisic-acid ; Amino Acid Sequence ; amino acid sequences ; Amino acids ; Arabidopsis - drug effects ; Arabidopsis - genetics ; Arabidopsis - radiation effects ; Arabidopsis Proteins - chemistry ; Arabidopsis Proteins - classification ; Arabidopsis Proteins - genetics ; Arabidopsis thaliana ; Biological and medical sciences ; cell-differentiation ; DNA-binding ; Fundamental and applied biological sciences. Psychology ; gene duplication ; Gene Expression Profiling ; Gene expression regulation ; Gene Expression Regulation, Plant - drug effects ; Gene Expression Regulation, Plant - radiation effects ; Genes ; Genes. Genome ; Genetics, Genomics, and Molecular Evolution ; Genomes ; genomics ; HD-zip ; homeobox gene ; homeodomain proteins ; Homeodomain Proteins - chemistry ; Homeodomain Proteins - classification ; Homeodomain Proteins - genetics ; homeotic genes ; layer-specific gene ; leaf development ; leucine zipper ; Leucine Zippers - genetics ; Light ; light intensity ; MHC class I genes ; Molecular and cellular biology ; Molecular genetics ; molecular sequence data ; nucleotide sequences ; Phylogenetics ; Phylogeny ; Plant growth regulators ; plant proteins ; Plants ; protein ; RNA ; Seedlings ; sequence analysis ; Sequence Homology, Amino Acid ; transcription factors ; Transcription Factors - chemistry ; Transcription Factors - genetics ; transcriptional activation ; Water - pharmacology ; water-deficit</subject><ispartof>Plant physiology (Bethesda), 2005-09, Vol.139 (1), p.509-518</ispartof><rights>Copyright 2005 American Society of Plant Biologists</rights><rights>2005 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c612t-402506d4590e4affd93a1b623070b058356ed01513780c1868e89076cb1fba1a3</citedby><cites>FETCH-LOGICAL-c612t-402506d4590e4affd93a1b623070b058356ed01513780c1868e89076cb1fba1a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/4281883$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/4281883$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,58238,58471</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17098751$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16055682$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-114417$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-75969$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Henriksson, Eva</creatorcontrib><creatorcontrib>Olsson, Anna S.B</creatorcontrib><creatorcontrib>Johannesson, Henrik</creatorcontrib><creatorcontrib>Johansson, Henrik</creatorcontrib><creatorcontrib>Hanson, Johannes</creatorcontrib><creatorcontrib>Engström, Peter</creatorcontrib><creatorcontrib>Söderman, Eva</creatorcontrib><title>Homeodomain Leucine Zipper Class I Genes in Arabidopsis. Expression Patterns and Phylogenetic Relationships</title><title>Plant physiology (Bethesda)</title><addtitle>Plant Physiol</addtitle><description>Members of the homeodomain leucine zipper (HDZip) family of transcription factors are present in a wide range of plants, from mosses to higher plants, but not in other eukaryotes. The HDZip genes act in developmental processes, including vascular tissue and trichome development, and several of them have been suggested to be involved in the mediation of external signals to regulate plant growth. The Arabidopsis (Arabidopsis thaliana) genome contains 47 HDZip genes, which, based on sequence criteria, have been grouped into four different classes: HDZip I to IV. In this article, we present an overview of the class I HDZip genes in Arabidopsis. We describe their expression patterns, transcriptional regulation properties, duplication history, and phylogeny. The phylogeny of HDZip class I genes is supported by data on the duplication history of the genes, as well as the intron/exon patterning of the HDZip-encoding motifs. The HDZip class I genes were found to be widely expressed and partly to have overlapping expression patterns at the organ level. Further, abscisic acid or water deficit treatments and different light conditions affected the transcript levels of a majority of the HDZip I genes. Within the gene family, our data show examples of closely related HDZip genes with similarities in the function of the gene product, but a divergence in expression pattern. In addition, six HDZip class I proteins tested were found to be activators of gene expression. In conclusion, several HDZip I genes appear to regulate similar cellular processes, although in different organs or tissues and in response to different environmental signals.</description><subject>abscisic-acid</subject><subject>Amino Acid Sequence</subject><subject>amino acid sequences</subject><subject>Amino acids</subject><subject>Arabidopsis - drug effects</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis - radiation effects</subject><subject>Arabidopsis Proteins - chemistry</subject><subject>Arabidopsis Proteins - classification</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis thaliana</subject><subject>Biological and medical sciences</subject><subject>cell-differentiation</subject><subject>DNA-binding</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>gene duplication</subject><subject>Gene Expression Profiling</subject><subject>Gene expression regulation</subject><subject>Gene Expression Regulation, Plant - drug effects</subject><subject>Gene Expression Regulation, Plant - radiation effects</subject><subject>Genes</subject><subject>Genes. Genome</subject><subject>Genetics, Genomics, and Molecular Evolution</subject><subject>Genomes</subject><subject>genomics</subject><subject>HD-zip</subject><subject>homeobox gene</subject><subject>homeodomain proteins</subject><subject>Homeodomain Proteins - chemistry</subject><subject>Homeodomain Proteins - classification</subject><subject>Homeodomain Proteins - genetics</subject><subject>homeotic genes</subject><subject>layer-specific gene</subject><subject>leaf development</subject><subject>leucine zipper</subject><subject>Leucine Zippers - genetics</subject><subject>Light</subject><subject>light intensity</subject><subject>MHC class I genes</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>molecular sequence data</subject><subject>nucleotide sequences</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant growth regulators</subject><subject>plant proteins</subject><subject>Plants</subject><subject>protein</subject><subject>RNA</subject><subject>Seedlings</subject><subject>sequence analysis</subject><subject>Sequence Homology, Amino Acid</subject><subject>transcription factors</subject><subject>Transcription Factors - chemistry</subject><subject>Transcription Factors - genetics</subject><subject>transcriptional activation</subject><subject>Water - pharmacology</subject><subject>water-deficit</subject><issn>0032-0889</issn><issn>1532-2548</issn><issn>1532-2548</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><recordid>eNqN0k1v1DAQBuAIgehSOHJDkAtc0C4z8Uec42opbaWVqIBy4GI5ibN1SWLjSQT997jaVfcIJ4_0Pn5laZxlLxFWiMA_hLBCECuQjEt8lC1QsGJZCK4eZwuANINS1Un2jOgWAJAhf5qdoAQhpCoW2c8LP1jf-sG4Md_auXGjzX-4EGzMN70hyi_zcztaylO-jqZ2rQ_kaJWf_QnREjk_5ldmmmwcKTdjm1_d3PV-l65Mrsm_2N5MidCNC_Q8e9KZnuyLw3maXX86-7a5WG4_n19u1ttlI7GYlhwKAbLlogLLTde1FTNYy4JBCTUIxYS0LaBAVipoUEllVQWlbGrsaoOGnWbv973024a51iG6wcQ77Y3TH933tfZxp-dZl6KSVdLL_9DDrBE5xzL5d3sfov81W5r04KixfW9G62fSUgmlOMN_wgKRVWXJjy9ooieKtnt4A4K-X7IOIY1C75ec_OtD8VwPtj3qw1YTeHsAhhrTd9GMjaOjK6FSpbgverV3tzT5-JDzQqFSLMVv9nFnvDa7mCquvxbpDwFCUQrg7C-0zcF0</recordid><startdate>20050901</startdate><enddate>20050901</enddate><creator>Henriksson, Eva</creator><creator>Olsson, Anna S.B</creator><creator>Johannesson, Henrik</creator><creator>Johansson, Henrik</creator><creator>Hanson, Johannes</creator><creator>Engström, Peter</creator><creator>Söderman, Eva</creator><general>American Society of Plant Biologists</general><general>American Society of Plant Physiologists</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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>D93</scope><scope>DF2</scope></search><sort><creationdate>20050901</creationdate><title>Homeodomain Leucine Zipper Class I Genes in Arabidopsis. Expression Patterns and Phylogenetic Relationships</title><author>Henriksson, Eva ; Olsson, Anna S.B ; Johannesson, Henrik ; Johansson, Henrik ; Hanson, Johannes ; Engström, Peter ; Söderman, Eva</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c612t-402506d4590e4affd93a1b623070b058356ed01513780c1868e89076cb1fba1a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>abscisic-acid</topic><topic>Amino Acid Sequence</topic><topic>amino acid sequences</topic><topic>Amino acids</topic><topic>Arabidopsis - drug effects</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis - radiation effects</topic><topic>Arabidopsis Proteins - chemistry</topic><topic>Arabidopsis Proteins - classification</topic><topic>Arabidopsis Proteins - genetics</topic><topic>Arabidopsis thaliana</topic><topic>Biological and medical sciences</topic><topic>cell-differentiation</topic><topic>DNA-binding</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>gene duplication</topic><topic>Gene Expression Profiling</topic><topic>Gene expression regulation</topic><topic>Gene Expression Regulation, Plant - drug effects</topic><topic>Gene Expression Regulation, Plant - radiation effects</topic><topic>Genes</topic><topic>Genes. Genome</topic><topic>Genetics, Genomics, and Molecular Evolution</topic><topic>Genomes</topic><topic>genomics</topic><topic>HD-zip</topic><topic>homeobox gene</topic><topic>homeodomain proteins</topic><topic>Homeodomain Proteins - chemistry</topic><topic>Homeodomain Proteins - classification</topic><topic>Homeodomain Proteins - genetics</topic><topic>homeotic genes</topic><topic>layer-specific gene</topic><topic>leaf development</topic><topic>leucine zipper</topic><topic>Leucine Zippers - genetics</topic><topic>Light</topic><topic>light intensity</topic><topic>MHC class I genes</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>molecular sequence data</topic><topic>nucleotide sequences</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant growth regulators</topic><topic>plant proteins</topic><topic>Plants</topic><topic>protein</topic><topic>RNA</topic><topic>Seedlings</topic><topic>sequence analysis</topic><topic>Sequence Homology, Amino Acid</topic><topic>transcription factors</topic><topic>Transcription Factors - chemistry</topic><topic>Transcription Factors - genetics</topic><topic>transcriptional activation</topic><topic>Water - pharmacology</topic><topic>water-deficit</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Henriksson, Eva</creatorcontrib><creatorcontrib>Olsson, Anna S.B</creatorcontrib><creatorcontrib>Johannesson, Henrik</creatorcontrib><creatorcontrib>Johansson, Henrik</creatorcontrib><creatorcontrib>Hanson, Johannes</creatorcontrib><creatorcontrib>Engström, Peter</creatorcontrib><creatorcontrib>Söderman, Eva</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>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Umeå universitet</collection><collection>SWEPUB Uppsala universitet</collection><jtitle>Plant physiology (Bethesda)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Henriksson, Eva</au><au>Olsson, Anna S.B</au><au>Johannesson, Henrik</au><au>Johansson, Henrik</au><au>Hanson, Johannes</au><au>Engström, Peter</au><au>Söderman, Eva</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Homeodomain Leucine Zipper Class I Genes in Arabidopsis. Expression Patterns and Phylogenetic Relationships</atitle><jtitle>Plant physiology (Bethesda)</jtitle><addtitle>Plant Physiol</addtitle><date>2005-09-01</date><risdate>2005</risdate><volume>139</volume><issue>1</issue><spage>509</spage><epage>518</epage><pages>509-518</pages><issn>0032-0889</issn><issn>1532-2548</issn><eissn>1532-2548</eissn><coden>PPHYA5</coden><abstract>Members of the homeodomain leucine zipper (HDZip) family of transcription factors are present in a wide range of plants, from mosses to higher plants, but not in other eukaryotes. The HDZip genes act in developmental processes, including vascular tissue and trichome development, and several of them have been suggested to be involved in the mediation of external signals to regulate plant growth. The Arabidopsis (Arabidopsis thaliana) genome contains 47 HDZip genes, which, based on sequence criteria, have been grouped into four different classes: HDZip I to IV. In this article, we present an overview of the class I HDZip genes in Arabidopsis. We describe their expression patterns, transcriptional regulation properties, duplication history, and phylogeny. The phylogeny of HDZip class I genes is supported by data on the duplication history of the genes, as well as the intron/exon patterning of the HDZip-encoding motifs. The HDZip class I genes were found to be widely expressed and partly to have overlapping expression patterns at the organ level. Further, abscisic acid or water deficit treatments and different light conditions affected the transcript levels of a majority of the HDZip I genes. Within the gene family, our data show examples of closely related HDZip genes with similarities in the function of the gene product, but a divergence in expression pattern. In addition, six HDZip class I proteins tested were found to be activators of gene expression. In conclusion, several HDZip I genes appear to regulate similar cellular processes, although in different organs or tissues and in response to different environmental signals.</abstract><cop>Rockville, MD</cop><pub>American Society of Plant Biologists</pub><pmid>16055682</pmid><doi>10.1104/pp.105.063461</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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subjects | abscisic-acid Amino Acid Sequence amino acid sequences Amino acids Arabidopsis - drug effects Arabidopsis - genetics Arabidopsis - radiation effects Arabidopsis Proteins - chemistry Arabidopsis Proteins - classification Arabidopsis Proteins - genetics Arabidopsis thaliana Biological and medical sciences cell-differentiation DNA-binding Fundamental and applied biological sciences. Psychology gene duplication Gene Expression Profiling Gene expression regulation Gene Expression Regulation, Plant - drug effects Gene Expression Regulation, Plant - radiation effects Genes Genes. Genome Genetics, Genomics, and Molecular Evolution Genomes genomics HD-zip homeobox gene homeodomain proteins Homeodomain Proteins - chemistry Homeodomain Proteins - classification Homeodomain Proteins - genetics homeotic genes layer-specific gene leaf development leucine zipper Leucine Zippers - genetics Light light intensity MHC class I genes Molecular and cellular biology Molecular genetics molecular sequence data nucleotide sequences Phylogenetics Phylogeny Plant growth regulators plant proteins Plants protein RNA Seedlings sequence analysis Sequence Homology, Amino Acid transcription factors Transcription Factors - chemistry Transcription Factors - genetics transcriptional activation Water - pharmacology water-deficit |
title | Homeodomain Leucine Zipper Class I Genes in Arabidopsis. Expression Patterns and Phylogenetic Relationships |
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