Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant

Bonawitz, Nicholas D.; Kim, Jeong Im; Tobimatsu, Yuki; Ciesielski, Peter N.; Anderson, Nickolas; Ximenes, Eduardo; Maeda, Jun; Ralph, John; Donohoe, Bryon S.; Ladisch, Michael R.; Chapple, Clint

doi:10.1038/nature13084

Cited by 325 publications

(350 citation statements)

References 37 publications

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“…MED5A was recently associated with lignin formation; the med5a mutation rescued the stunted growth, collapsed xylem vessels, and lignin deficiency phenotypes in the Arabidopsis phenylpropanoid pathway mutant ref8-1 (ref. 61 Table 18). A second component of the same mediator complex that appears among the putatively swept genes is MED12, which is involved in flowering time regulation in Arabidopsis 62 .…”

Section: Candidate Gene Adaptation Correlates With Environmentmentioning

confidence: 99%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

246

253

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Forest ecosystems maintain a large share of Northern Hemisphere biodiversity. Boreal forests comprise roughly 30% of global forest area 1 and contain the highest tree density among climate zones 2 . Moreover, boreal regions are undergoing extensive climate change. Annual temperature increases exceeding 1.5 °C are projected to result in a warming of 4-11 °C by the end of this century, with little concomitant increase in precipitation 1 . At this pace, climate zones will shift northward at a greater speed than trees can migrate 3 . To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes. Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch.Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightlylinked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.A full list of affiliations appears at the end of the paper.

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Section: Candidate Gene Adaptation Correlates With Environmentmentioning

confidence: 99%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

246

253

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“…The recent biochemical isolation of the plant Mediator complex from Arabidopsis (19) significantly facilitated the characterization of the diverse functions of individual plant Mediator subunits (38)(39)(40). However, a thorough mechanistic understanding of plant Mediator function remains elusive.…”

Section: Discussionmentioning

confidence: 99%

Mediator subunit MED25 links the jasmonate receptor to transcriptionally active chromatin

Lin

Zhai

et al. 2017

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

150

180

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Jasmonoyl-isoleucine (JA-Ile), the active form of the plant hormone jasmonate (JA), is sensed by the F-box protein CORONATINE INSENSITIVE 1 (COI1), a component of a functional Skp-Cullin-F-box E3 ubiquitin ligase complex. Sensing of JA-Ile by COI1 rapidly triggers genome-wide transcriptional changes that are largely regulated by the basic helix-loop-helix transcription factor MYC2. However, it remains unclear how the JA-Ile receptor protein COI1 relays hormone-specific regulatory signals to the RNA polymerase II general transcriptional machinery. Here, we report that the plant transcriptional coactivator complex Mediator directly links COI1 to the promoters of MYC2 target genes. MED25, a subunit of the Mediator complex, brings COI1 to MYC2 target promoters and facilitates COI1-dependent degradation of jasmonate-ZIM domain (JAZ) transcriptional repressors. MED25 and COI1 influence each other's enrichment on MYC2 target promoters. Furthermore, MED25 physically and functionally interacts with HISTONE ACETYLTRANSFERASE1 (HAC1), which plays an important role in JA signaling by selectively regulating histone (H) 3 lysine (K) 9 (H3K9) acetylation of MYC2 target promoters. Moreover, the enrichment and function of HAC1 on MYC2 target promoters depend on COI1 and MED25. Therefore, the MED25 interface of Mediator links COI1 with HAC1-dependent H3K9 acetylation to activate MYC2-regulated transcription of JAresponsive genes. This study exemplifies how a single Mediator subunit integrates the actions of both genetic and epigenetic regulators into a concerted transcriptional program.is an oxylipin-derived plant hormone that regulates diverse aspects of plant immunity and development (1, 2). Decades of studies in the model plant Arabidopsis thaliana have revealed a core JA signaling module consisting of the F-box protein CORONATINE INSENSITIVE 1 (COI1) (3), a group of jasmonate-ZIM domain (JAZ) proteins (4-6), and the basic helixloop-helix transcription factor MYC2 (7, 8). COI1 forms a functional Skp-Cullin-F-box (SCF) E3 ubiquitin ligase SCF COI1 along with Cullin1 and Skp1-like1 (ASK1) (9, 10), MYC2 acts as a master transcription factor that differentially regulates diverse aspects of JA responses (11-13), and the JAZ proteins are substrates of SCF COI1 and serve as transcriptional repressors of MYC2 (4, 5, 14). The identification of jasmonoyl-isoleucine (JA-Ile) as the receptor-active form of the hormone, along with the discovery that sensing of JA-Ile involves formation of the SCF COI1 -JAZs coreceptor complex (4, 15-17), represented a breakthrough in our mechanistic understanding of JA signaling. In the absence of the hormone, JAZ repressors interact with and repress the activity of MYC2. In response to internal or external cues that trigger JAIle synthesis, elevated JA-Ile levels promote SCF COI1 -dependent degradation of JAZ repressors, and thereby activate (de-repress) the MYC2-directed transcriptional program. These discoveries imply that sensing of the active hormone is tightly linked to transcription of JA-responsive...

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“…The data support that a mechanism exists, possibly mediated by apoplastic H 2 O 2 , sensing a reduced need for monolignol biosynthesis under H 2 O 2 -scavenging conditions when monolignols cannot polymerize, whereas under more oxidative conditions, the synthesis of monolignols is up-regulated. Alternatively, the signal can be a phenolic compound (Bonawitz et al, 2014). The differential expression analysis revealed several CRK-encoding genes that were up-regulated in ligninforming conditions (Fig.…”

Section: The Apoplastic Redox State Influences Cellular Metabolismmentioning

confidence: 99%

A Key Role for Apoplastic H₂O₂ in Norway Spruce Phenolic Metabolism

et al. 2017

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Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic hydrogen peroxide (H 2 O 2 ) in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H 2 O 2 by potassium iodide repressed lignin formation, in line with peroxidases activating monolignols for lignin polymerization. Time-course analyses coupled to candidate substrate-product pair network propagation revealed differential accumulation of low-molecular-weight phenolics, including (glycosylated) oligolignols, (glycosylated) flavonoids, and proanthocyanidins, in lignin-forming and H 2 O 2 -scavenging cultures and supported that monolignols are oxidatively coupled not only in the cell wall but also in the cytoplasm, where they are coupled to other monolignols and proanthocyanidins. Dilignol glycoconjugates with reduced structures were found in the culture medium, suggesting that cells are able to transport glycosylated dilignols to the apoplast. Transcriptomic analyses revealed that scavenging of apoplastic H 2 O 2 resulted in remodulation of the transcriptome, with reduced carbon flux into the shikimate pathway propagating down to monolignol biosynthesis. Aggregated coexpression network analysis identified candidate enzymes and transcription factors for monolignol oxidation and apoplastic H 2 O 2 production in addition to potential H 2 O 2 receptors. The results presented indicate that the redox state of the apoplast has a profound influence on cellular metabolism.

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Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant

Cited by 325 publications

References 37 publications

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Mediator subunit MED25 links the jasmonate receptor to transcriptionally active chromatin

A Key Role for Apoplastic H₂O₂ in Norway Spruce Phenolic Metabolism

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Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant

Cited by 325 publications

References 37 publications

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Mediator subunit MED25 links the jasmonate receptor to transcriptionally active chromatin

A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism

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A Key Role for Apoplastic H₂O₂ in Norway Spruce Phenolic Metabolism