Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression
Natural light environments are highly variable. Flexible adjustment between light energy utilization and photoprotection is therefore of vital importance for plant performance and fitness in the field. Short-term reactions to changing light intensity are triggered inside chloroplasts and leaves with...
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Veröffentlicht in: | Plant physiology (Bethesda) 2019-04, Vol.179 (4), p.1632-1657 |
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description | Natural light environments are highly variable. Flexible adjustment between light energy utilization and photoprotection is therefore of vital importance for plant performance and fitness in the field. Short-term reactions to changing light intensity are triggered inside chloroplasts and leaves within seconds to minutes, whereas long-term adjustments proceed over hours and days, integrating multiple signals. While the mechanisms of long-term acclimation to light intensity have been studied by changing constant growth light intensity during the day, responses to fluctuating growth light intensity have rarely been inspected in detail. We performed transcriptome profiling in Arabidopsis (Arabidopsis thaliana) leaves to investigate long-term gene expression responses to fluctuating light (FL). In particular, we examined whether responses differ between young and mature leaves or between morning and the end of the day. Our results highlight global reprogramming of gene expression under FL, including that of genes related to photoprotection, photosynthesis, and photorespiration and to pigment, prenylquinone, and vitamin metabolism. The FL-induced changes in gene expression varied between young and mature leaves at the same time point and between the same leaves in the morning and at the end of the day, indicating interactions of FL acclimation with leaf development stage and time of day. Only 46 genes were up- or down-regulated in both young and mature leaves at both time points. Combined analyses of gene coexpression and cis-elements pointed to a role of the circadian clock and light in coordinating the acclimatory responses of functionally related genes. Our results also suggest a possible cross talk between FL acclimation and systemic acquired resistance-like gene expression in young leaves. |
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Flexible adjustment between light energy utilization and photoprotection is therefore of vital importance for plant performance and fitness in the field. Short-term reactions to changing light intensity are triggered inside chloroplasts and leaves within seconds to minutes, whereas long-term adjustments proceed over hours and days, integrating multiple signals. While the mechanisms of long-term acclimation to light intensity have been studied by changing constant growth light intensity during the day, responses to fluctuating growth light intensity have rarely been inspected in detail. We performed transcriptome profiling in Arabidopsis (Arabidopsis thaliana) leaves to investigate long-term gene expression responses to fluctuating light (FL). In particular, we examined whether responses differ between young and mature leaves or between morning and the end of the day. Our results highlight global reprogramming of gene expression under FL, including that of genes related to photoprotection, photosynthesis, and photorespiration and to pigment, prenylquinone, and vitamin metabolism. The FL-induced changes in gene expression varied between young and mature leaves at the same time point and between the same leaves in the morning and at the end of the day, indicating interactions of FL acclimation with leaf development stage and time of day. Only 46 genes were up- or down-regulated in both young and mature leaves at both time points. Combined analyses of gene coexpression and cis-elements pointed to a role of the circadian clock and light in coordinating the acclimatory responses of functionally related genes. Our results also suggest a possible cross talk between FL acclimation and systemic acquired resistance-like gene expression in young leaves.</description><identifier>ISSN: 0032-0889</identifier><identifier>EISSN: 1532-2548</identifier><identifier>DOI: 10.1104/pp.18.01443</identifier><identifier>PMID: 30718349</identifier><language>eng</language><publisher>United States: American Society of Plant Biologists (ASPB)</publisher><subject>Acclimatization - genetics ; Arabidopsis - genetics ; Arabidopsis - growth & development ; Arabidopsis - radiation effects ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; Arabidopsis Proteins - physiology ; ECOPHYSIOLOGY AND SUSTAINABILITY ; Gene Expression Profiling ; Gene Expression Regulation, Plant - radiation effects ; Oxidative Stress - genetics ; Oxidative Stress - radiation effects ; Photosynthesis - genetics ; Plant Leaves - genetics ; Plant Leaves - growth & development ; Plant Leaves - radiation effects ; Sunlight ; Time Factors</subject><ispartof>Plant physiology (Bethesda), 2019-04, Vol.179 (4), p.1632-1657</ispartof><rights>2019 American Society of Plant Biologists</rights><rights>2019 American Society of Plant Biologists. All Rights Reserved.</rights><rights>2019 American Society of Plant Biologists. All Rights Reserved. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c403t-5177bcbc9116bff084eaa0816352da2ade2128030449d796dbac425e9a587e453</citedby><orcidid>0000-0002-0272-6580 ; 0000-0002-1440-6496 ; 0000-0002-0352-2547 ; 0000-0002-8703-5403 ; 0000-0003-1566-7572</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,778,782,883,27911,27912</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30718349$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schneider, Trang</creatorcontrib><creatorcontrib>Bolger, Anthony</creatorcontrib><creatorcontrib>Zeier, Jürgen</creatorcontrib><creatorcontrib>Preiskowski, Sabine</creatorcontrib><creatorcontrib>Benes, Vladimir</creatorcontrib><creatorcontrib>Trenkamp, Sandra</creatorcontrib><creatorcontrib>Usadel, Björn</creatorcontrib><creatorcontrib>Farré, Eva M.</creatorcontrib><creatorcontrib>Matsubaraa, Shizue</creatorcontrib><title>Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression</title><title>Plant physiology (Bethesda)</title><addtitle>Plant Physiol</addtitle><description>Natural light environments are highly variable. Flexible adjustment between light energy utilization and photoprotection is therefore of vital importance for plant performance and fitness in the field. Short-term reactions to changing light intensity are triggered inside chloroplasts and leaves within seconds to minutes, whereas long-term adjustments proceed over hours and days, integrating multiple signals. While the mechanisms of long-term acclimation to light intensity have been studied by changing constant growth light intensity during the day, responses to fluctuating growth light intensity have rarely been inspected in detail. We performed transcriptome profiling in Arabidopsis (Arabidopsis thaliana) leaves to investigate long-term gene expression responses to fluctuating light (FL). In particular, we examined whether responses differ between young and mature leaves or between morning and the end of the day. Our results highlight global reprogramming of gene expression under FL, including that of genes related to photoprotection, photosynthesis, and photorespiration and to pigment, prenylquinone, and vitamin metabolism. The FL-induced changes in gene expression varied between young and mature leaves at the same time point and between the same leaves in the morning and at the end of the day, indicating interactions of FL acclimation with leaf development stage and time of day. Only 46 genes were up- or down-regulated in both young and mature leaves at both time points. Combined analyses of gene coexpression and cis-elements pointed to a role of the circadian clock and light in coordinating the acclimatory responses of functionally related genes. Our results also suggest a possible cross talk between FL acclimation and systemic acquired resistance-like gene expression in young leaves.</description><subject>Acclimatization - genetics</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis - growth & development</subject><subject>Arabidopsis - radiation effects</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis Proteins - metabolism</subject><subject>Arabidopsis Proteins - physiology</subject><subject>ECOPHYSIOLOGY AND SUSTAINABILITY</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant - radiation effects</subject><subject>Oxidative Stress - genetics</subject><subject>Oxidative Stress - radiation effects</subject><subject>Photosynthesis - genetics</subject><subject>Plant Leaves - genetics</subject><subject>Plant Leaves - growth & development</subject><subject>Plant Leaves - radiation effects</subject><subject>Sunlight</subject><subject>Time Factors</subject><issn>0032-0889</issn><issn>1532-2548</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkc1v1DAQxS1ERZfCiTPIRyS0i8d2HOeChPpFpZWQoJwtx5lkXSVxsJ1C__um3bIqp5nR--nNkx4h74BtAJj8PE0b0BsGUooXZAWF4GteSP2SrBhbdqZ1dUxep3TDGAMB8hU5FqwELWS1Is1FP7s82-zHjm59t8v0aswYrcuJ_vF5R6_9gDS09MzeUTs2dIt2OfAW-zANOGb6M9sOaQ70B04xdNEO9BJHpOd_p4gp-TC-IUet7RO-fZon5NfF-fXpt_X2--XV6dft2kkm8rqAsqxd7SoAVbct0xKtZRqUKHhjuW2QA9dMMCmrpqxUU1sneYGVLXSJshAn5Mved5rrARu3pIu2N1P0g413Jlhv_ldGvzNduDVKSlUqWAw-PhnE8HvGlM3gk8O-tyOGORkOZVWAqpRa0E971MWQUsT28AaYeejFTJMBbR57WegPz5Md2H9FLMD7PXCTcogHnauSLYWCuAfS2ZM9</recordid><startdate>20190401</startdate><enddate>20190401</enddate><creator>Schneider, Trang</creator><creator>Bolger, Anthony</creator><creator>Zeier, Jürgen</creator><creator>Preiskowski, Sabine</creator><creator>Benes, Vladimir</creator><creator>Trenkamp, Sandra</creator><creator>Usadel, Björn</creator><creator>Farré, Eva M.</creator><creator>Matsubaraa, Shizue</creator><general>American Society of Plant Biologists (ASPB)</general><general>American Society of Plant Biologists</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>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-0272-6580</orcidid><orcidid>https://orcid.org/0000-0002-1440-6496</orcidid><orcidid>https://orcid.org/0000-0002-0352-2547</orcidid><orcidid>https://orcid.org/0000-0002-8703-5403</orcidid><orcidid>https://orcid.org/0000-0003-1566-7572</orcidid></search><sort><creationdate>20190401</creationdate><title>Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression</title><author>Schneider, Trang ; Bolger, Anthony ; Zeier, Jürgen ; Preiskowski, Sabine ; Benes, Vladimir ; Trenkamp, Sandra ; Usadel, Björn ; Farré, Eva M. ; Matsubaraa, Shizue</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c403t-5177bcbc9116bff084eaa0816352da2ade2128030449d796dbac425e9a587e453</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Acclimatization - genetics</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis - growth & development</topic><topic>Arabidopsis - radiation effects</topic><topic>Arabidopsis Proteins - genetics</topic><topic>Arabidopsis Proteins - metabolism</topic><topic>Arabidopsis Proteins - physiology</topic><topic>ECOPHYSIOLOGY AND SUSTAINABILITY</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant - radiation effects</topic><topic>Oxidative Stress - genetics</topic><topic>Oxidative Stress - radiation effects</topic><topic>Photosynthesis - genetics</topic><topic>Plant Leaves - genetics</topic><topic>Plant Leaves - growth & development</topic><topic>Plant Leaves - radiation effects</topic><topic>Sunlight</topic><topic>Time Factors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schneider, Trang</creatorcontrib><creatorcontrib>Bolger, Anthony</creatorcontrib><creatorcontrib>Zeier, Jürgen</creatorcontrib><creatorcontrib>Preiskowski, Sabine</creatorcontrib><creatorcontrib>Benes, Vladimir</creatorcontrib><creatorcontrib>Trenkamp, Sandra</creatorcontrib><creatorcontrib>Usadel, Björn</creatorcontrib><creatorcontrib>Farré, Eva M.</creatorcontrib><creatorcontrib>Matsubaraa, Shizue</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Plant physiology (Bethesda)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schneider, Trang</au><au>Bolger, Anthony</au><au>Zeier, Jürgen</au><au>Preiskowski, Sabine</au><au>Benes, Vladimir</au><au>Trenkamp, Sandra</au><au>Usadel, Björn</au><au>Farré, Eva M.</au><au>Matsubaraa, Shizue</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression</atitle><jtitle>Plant physiology (Bethesda)</jtitle><addtitle>Plant Physiol</addtitle><date>2019-04-01</date><risdate>2019</risdate><volume>179</volume><issue>4</issue><spage>1632</spage><epage>1657</epage><pages>1632-1657</pages><issn>0032-0889</issn><eissn>1532-2548</eissn><abstract>Natural light environments are highly variable. Flexible adjustment between light energy utilization and photoprotection is therefore of vital importance for plant performance and fitness in the field. Short-term reactions to changing light intensity are triggered inside chloroplasts and leaves within seconds to minutes, whereas long-term adjustments proceed over hours and days, integrating multiple signals. While the mechanisms of long-term acclimation to light intensity have been studied by changing constant growth light intensity during the day, responses to fluctuating growth light intensity have rarely been inspected in detail. We performed transcriptome profiling in Arabidopsis (Arabidopsis thaliana) leaves to investigate long-term gene expression responses to fluctuating light (FL). In particular, we examined whether responses differ between young and mature leaves or between morning and the end of the day. Our results highlight global reprogramming of gene expression under FL, including that of genes related to photoprotection, photosynthesis, and photorespiration and to pigment, prenylquinone, and vitamin metabolism. The FL-induced changes in gene expression varied between young and mature leaves at the same time point and between the same leaves in the morning and at the end of the day, indicating interactions of FL acclimation with leaf development stage and time of day. Only 46 genes were up- or down-regulated in both young and mature leaves at both time points. Combined analyses of gene coexpression and cis-elements pointed to a role of the circadian clock and light in coordinating the acclimatory responses of functionally related genes. 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subjects | Acclimatization - genetics Arabidopsis - genetics Arabidopsis - growth & development Arabidopsis - radiation effects Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Arabidopsis Proteins - physiology ECOPHYSIOLOGY AND SUSTAINABILITY Gene Expression Profiling Gene Expression Regulation, Plant - radiation effects Oxidative Stress - genetics Oxidative Stress - radiation effects Photosynthesis - genetics Plant Leaves - genetics Plant Leaves - growth & development Plant Leaves - radiation effects Sunlight Time Factors |
title | Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression |
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