Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth

Wei, Hairong; Gou, Jiqing; Yordanov, Yordan S.; Zhang, Huaxin; Thakur, Ramesh; Jones, Wendy S.; Burton, Andrew J.

doi:10.1007/s10265-012-0524-4

Cited by 41 publications

(56 citation statements)

References 75 publications

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“…To identify overrepresented gene families among the DEGs, we performed a domain enrichment analysis (29). Several protein families were overrepresented, including 20 laccases (types 1, 2, and 3 multicopper oxidases), 7 peroxidases, and 4 chalcone/stilbene synthases (Table S4).…”

Section: Down-regulation Of Ptrlac Transcript Abundance By Overexpresmentioning

confidence: 99%

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

Wei

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Laccases, as early as 1959, were proposed to catalyze the oxidative polymerization of monolignols. Genetic evidence in support of this hypothesis has been elusive due to functional redundancy of laccase genes. An Arabidopsis double mutant demonstrated the involvement of laccases in lignin biosynthesis. We previously identified a subset of laccase genes to be targets of a microRNA (miRNA) ptr-miR397a in Populus trichocarpa. To elucidate the roles of ptr-miR397a and its targets, we characterized the laccase gene family and identified 49 laccase gene models, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed PtrMIR397a in transgenic P. trichocarpa. In each of all nine transgenic lines tested, 17 PtrLACs were down-regulated as analyzed by RNAseq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an ∼40% decrease in the total laccase activity. Overexpression of Ptr-MIR397a in these transgenic lines also reduced lignin content, whereas levels of all monolignol biosynthetic gene transcripts remained unchanged. A hierarchical genetic regulatory network (GRN) built by a bottom-up graphic Gaussian model algorithm provides additional support for a role of ptr-miR397a as a negative regulator of laccases for lignin biosynthesis. Full transcriptome-based differential gene expression in the overexpressed transgenics and protein domain analyses implicate previously unidentified transcription factors and their targets in an extended hierarchical GRN including ptr-miR397a and laccases that coregulate lignin biosynthesis in wood formation. Ptr-miR397a, laccases, and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content.L ignin, an abundant biological polymer affecting the ecology of the terrestrial biosphere, is vital for the integrity of plant cell walls, the strength of stems, and resistance against pests and pathogens (1). Lignin is also a major barrier in the pulping and biomass-to-ethanol processes (2-4). For extracting cellulose (pulping) or for enzymatic degradation of cellulose for bioethanol, harsh chemical or physical treatments are used to reduce interactions with lignin or other cell wall components (2-4). Reducing lignin content or altering lignin structure to reduce its recalcitrance are major goals for more efficient processing.Lignin is polymerized primarily from three monolignol precursors, p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol (1, 5). Over five decades, efforts have been made to understand the biosynthesis of the primary monolignols and to modify the quantity or composition of lignin. The polymerization of monolignols into a lignin polymer has long been thought to occur through oxidative polymerization catalyzed by either laccases or peroxidases (6). The mechanisms and specificity of the roles of the oxidative enzymes in lignin polymerization have been controversial (7).Laccases (EC. 1.10.3.2) are multicopper oxidoreductases. Plant laccase was the first enzyme sh...

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Section: Down-regulation Of Ptrlac Transcript Abundance By Overexpresmentioning

confidence: 99%

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

Wei

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

337

339

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“…Similarly, large number of studies on genome-wide expression profiling of plants grown under high [CO 2 ] have been carried out Leakey et al, 2009;Cseke et al, 2009;Wei et al, 2013). Ribeiro et al (2013) showed that high [CO 2 ] promote plant growth via a complex transcriptional network.…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

Physiological and molecular alterations in plants exposed to high [CO2] under phosphorus stress

Pandey

Zinta

AbdElgawad

et al. 2015

Biotechnology Advances

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Physiological and molecular alterations in plants exposed to high [CO 2 ] under phosphorus stress, Biotechnology Advances (2015Advances ( ), doi: 10.1016Advances ( /j.biotechadv.2015 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. This is the author's version of a work that was accepted for publication in Biotechnology Advances (Ed. Elsevier). Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Pandey, Renu et al. Fax: +91-11-25846420] has increased substantially in recent decades and will continue to do so, whereas the availability of phosphorus (P) is limited and unlikely to increase in the future. P is a non-renewable resource, and it is essential to every form of life. P is a key plant nutrient controlling the responsiveness of photosynthesis to [CO 2 ]. Increases in [CO 2 ] typically results in increased biomass through stimulation of net photosynthesis, and hence enhance the demand for P uptake. However, most soils contain low concentrations of available P.Therefore, low P is one of the major growth-limiting factors for plants in many agricultural and natural ecosystems. The adaptive responses of plants to [CO 2 ] and P availability encompass alterations at morphological, physiological, biochemical and molecular levels. In general low P reduces growth, whereas high [CO 2 ] enhances it particularly in C 3 plants. Photosynthetic capacity is often enhanced under high [CO

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“…The influence of elevated [CO 2 ] on the transcriptome is well characterised in trees such as Populus and Betula species [30][31][32][33]. In Populus, expression in leaves of up to 50 genes was changed by elevated [CO 2 ], depending on the developmental age of the leaves [30].…”

Section: Introductionmentioning

confidence: 99%

“…In Populus, expression in leaves of up to 50 genes was changed by elevated [CO 2 ], depending on the developmental age of the leaves [30]. Long term (12 years) exposure of Populus to elevated [CO 2 ] led to increased radial growth with enhanced expression of genes related to Calvin cycle activity and linked pathways in leaves, and the pathways involved in cell growth, cell division, hormone metabolism, and secondary cell wall formation were altered in the vascular cambium of the stem [32]. Pot experiments on Arabidopsis and sugarcane showed an influence of elevated [CO 2 ] on different metabolic pathways, mainly in relation to C-and N-metabolism and photosynthesis [34,35].…”

Section: Introductionmentioning

confidence: 99%

Expression patterns of C- and N-metabolism related genes in wheat are changed during senescence under elevated CO2 in dry-land agriculture

et al. 2015

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Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth

Cited by 41 publications

References 75 publications

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

Physiological and molecular alterations in plants exposed to high [CO2] under phosphorus stress

Expression patterns of C- and N-metabolism related genes in wheat are changed during senescence under elevated CO2 in dry-land agriculture

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