ATTED-II provides coexpressed gene networks for Arabidopsis

Obayashi, Takeshi; Hayashi, Shinji; Saeki, Motoshi; Ohta, Hiroyuki; Kinoshita, Kengo

doi:10.1093/nar/gkn807

Cited by 331 publications

(316 citation statements)

References 28 publications

(32 reference statements)

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“…n.d., Not detected. soluble cytosolic protein (Arabidopsis database ATTEDII; Obayashi et al, 2009), a-DOX1-GFP was also detected on the leaf oil bodies (Fig. 1E).…”

Section: Identification Of A-dox1 As An Oil Body-localized Proteinmentioning

confidence: 96%

Leaf Oil Body Functions as a Subcellular Factory for the Production of a Phytoalexin in Arabidopsis

et al. 2013

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“…n.d., Not detected. soluble cytosolic protein (Arabidopsis database ATTEDII; Obayashi et al, 2009), a-DOX1-GFP was also detected on the leaf oil bodies (Fig. 1E).…”

Section: Identification Of A-dox1 As An Oil Body-localized Proteinmentioning

confidence: 96%

Leaf Oil Body Functions as a Subcellular Factory for the Production of a Phytoalexin in Arabidopsis

et al. 2013

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“…Furthermore, the transcriptionally regulated genes of the PAO pathway, i.e. SGR, NYC1, PPH, PAO and MES16 (Ren et al 2007(Ren et al , 2010Schelbert et al 2009;Pružinská et al 2005;Horie et al 2009;Christ et al 2012) are highly coregulated in Arabidopsis and consequently cluster closely together when performing gene network analyses, for example using the ATTEDII platform (Obayashi et al 2009). Possibly, among the hundreds of transcription factors that have been shown to be up-regulated during leaf senescence (Balazadeh et al 2008) are some that specifically target the PAO pathway, but these have so far not been identified.…”

Section: Gene Regulationmentioning

confidence: 99%

Update on the biochemistry of chlorophyll breakdown

2012

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In land plants, chlorophyll is broken down to colorless linear tetrapyrroles in a highly conserved multi-step pathway. The pathway is termed the 'PAO pathway', because the opening of the chlorine macrocycle present in chlorophyll catalyzed by pheophorbide a oxygenase (PAO), the key enzyme of the pathway, provides the characteristic structural basis found in all further downstream chlorophyll breakdown products. To date, most of the biochemical steps of the PAO pathway have been elucidated and genes encoding many of the chlorophyll catabolic enzymes been identified. This review summarizes the current knowledge on the biochemistry of the PAO pathway and provides insight into recent progress made in the field that indicates that the pathway is more complex than thought in the past. Abstract In land plants, chlorophyll is broken down to colorless linear tetrapyrroles in a highly conserved multistep pathway. The pathway is termed the 'PAO pathway', because the opening of the chlorine macrocycle present in chlorophyll catalyzed by pheophorbide a oxygenase (PAO), the key enzyme of the pathway, provides the characteristic structural basis found in all further downstream chlorophyll breakdown products. To date, most of the biochemical steps of the PAO pathway have been elucidated and genes encoding many of the chlorophyll catabolic enzymes been identified. This review summarizes the current knowledge on the biochemistry of the PAO pathway and provides insight into recent progress made in the field that indicates that the pathway is more complex than thought in the past.

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“…Thus, these HD-ZIP IVs have unique yet partially overlapping functions in specifying multiple aspects of epidermal development. Bioinformatic co-expression network ATTED II (Obayashi et al, 2009) places HDG2 at the 'hub' connecting stomatal and protodermal regulators: HDG2 clusters with SPCH, TMM and SCRM/ICE1, with a direct connection to SCRM/ICE1 (supplementary material Fig. S6).…”

Section: Research Articlementioning

confidence: 99%

Arabidopsishomeodomain-leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis

et al. 2013

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SUMMARYThe shoot epidermis of land plants serves as a crucial interface between plants and the atmosphere: pavement cells protect plants from desiccation and other environmental stresses, while stomata facilitate gas exchange and transpiration. Advances have been made in our understanding of stomatal patterning and differentiation, and a set of 'master regulatory' transcription factors of stomatal development have been identified. However, they are limited to specifying stomatal differentiation within the epidermis. Here, we report the identification of an Arabidopsis homeodomain-leucine zipper IV (HD-ZIP IV) protein, HOMEODOMAIN GLABROUS2 (HDG2), as a key epidermal component promoting stomatal differentiation. HDG2 is highly enriched in meristemoids, which are transient-amplifying populations of stomatal-cell lineages. Ectopic expression of HDG2 confers differentiation of stomata in internal mesophyll tissues and occasional multiple epidermal layers. Conversely, a loss-of-function hdg2 mutation delays stomatal differentiation and, rarely but consistently, results in aberrant stomata. A closely related HD-ZIP IV gene, Arabidopsis thaliana MERISTEM LAYER1 (AtML1), shares overlapping function with HDG2: AtML1 overexpression also triggers ectopic stomatal differentiation in the mesophyll layer and atml1 mutation enhances the stomatal differentiation defects of hdg2. Consistently, HDG2 and AtML1 bind the same DNA elements, and activate transcription in yeast. Furthermore, HDG2 transactivates expression of genes that regulate stomatal development in planta. Our study highlights the similarities and uniqueness of these two HD-ZIP IV genes in the specification of protodermal identity and stomatal differentiation beyond predetermined tissue layers.

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ATTED-II provides coexpressed gene networks for Arabidopsis

Cited by 331 publications

References 28 publications

Leaf Oil Body Functions as a Subcellular Factory for the Production of a Phytoalexin in Arabidopsis

Leaf Oil Body Functions as a Subcellular Factory for the Production of a Phytoalexin in Arabidopsis

Update on the biochemistry of chlorophyll breakdown

Arabidopsishomeodomain-leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis

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