PlantCARE, a plant cis-acting regulatory element database

Rombauts, Stéphane; Déhais, Patrice; Montagu, Marc Van; Rouzé, Pierre

doi:10.1093/nar/27.1.295

Cited by 533 publications

(326 citation statements)

References 10 publications

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“…We analyzed the promoter region 1,500 bp upstream of the start codon by using both the PLACE (Higo et al, 1998(Higo et al, , 1999 and PlantCARE (Rombauts et al, 1999;Lescot et al, 2002) software. As shown in Figure 1A, the existence of cis-acting regulatory elements of a sugarrepressive element (S), a phytochrome-regulation element (P), a CCA1-binding site (C), and a GA-responsive element (G) implied that AtTLP18.3 might be controlled by the circadian rhythm, Suc, and GA. We compared the diurnal expression patterns of AtTLP18.3 in CIR-CADIAN CLOCK-ASSOCIATED1 (CCA1)-overexpressing (CCA1-ox) mutants and wild-type Arabidopsis.…”

Section: Transcripts Of Attlp183 Followed a Diurnal Rhythmmentioning

confidence: 99%

Structural and Functional Assays of AtTLP18.3 Identify Its Novel Acid Phosphatase Activity in Thylakoid Lumen

Liu

Lin

et al. 2011

Plant Physiology

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The membrane protein AtTLP18.3 of Arabidopsis (Arabidopsis thaliana) contains a domain of unknown function, DUF477; it forms a polysome with photosynthetic apparatuses in the thylakoid lumen. To explore the molecular function of AtTLP18.3, we resolved its crystal structures with residues 83 to 260, the DUF477 only, and performed a series of biochemical analyses to discover its function. The gene expression of AtTLP18.3 followed a circadian rhythm. X-ray crystallography revealed the folding of AtTLP18.3 as a three-layer sandwich with three a-helices in the upper layer, four b-sheets in the middle layer, and two a-helices in the lower layer, which resembles a Rossmann fold. Structural comparison suggested that AtTLP18.3 might be a phosphatase. The enzymatic activity of AtTLP18.3 was further confirmed by phosphatase assay with various substrates (e.g. p-nitrophenyl phosphate, 6,8-difluoro-4-methylumbelliferyl phosphate, O-phospho-L-serine, and several synthetic phosphopeptides). Furthermore, we obtained the structure of AtTLP18.3 in complex with O-phospho-L-serine to identify the binding site of AtTLP18.3. Our structural and biochemical studies revealed that AtTLP18.3 has the molecular function of a novel acid phosphatase in the thylakoid lumen. DUF477 is accordingly renamed the thylakoid acid phosphatase domain.

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Section: Transcripts Of Attlp183 Followed a Diurnal Rhythmmentioning

confidence: 99%

Structural and Functional Assays of AtTLP18.3 Identify Its Novel Acid Phosphatase Activity in Thylakoid Lumen

Liu

Lin

et al. 2011

Plant Physiology

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“…Potential promoter sequences (2 kb upstream elements) were used to search for the Plant Cis-Acting Regulatory Elements Database (Rombauts et al, 1999; http://bioinformatics.psb.ugent.be/webtools/plantcare/html/).…”

Section: Promoter Predictionmentioning

confidence: 99%

A Novel Nuclear-Localized CCCH-Type Zinc Finger Protein, OsDOS, Is Involved in Delaying Leaf Senescence in Rice

et al. 2006

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Leaf senescence is a developmentally programmed degeneration process, which is fine tuned by a complex regulatory network for plant fitness. However, molecular regulation of leaf senescence is poorly understood, especially in rice (Oryza sativa), an important staple crop for more than half of the world population. Here, we report a novel nuclear-localized CCCH-type zinc finger protein, Oryza sativa delay of the onset of senescence (OsDOS), involved in delaying leaf senescence in rice. The expression of OsDOS was down-regulated during natural leaf senescence, panicle development, and pollination, although its transcripts were accumulated in various organs. RNAi knockdown of OsDOS caused an accelerated age-dependent leaf senescence, whereas its overexpression produced a marked delay of leaf senescence, suggesting that it acts as a negative regulator for leaf senescence. A genome-wide expression analysis further confirmed its negative regulation for leaf senescence and revealed that, in particular, the jasmonate (JA) pathway was found to be hyperactive in the OsDOS RNAi transgenic lines but impaired in the OsDOS overexpressing transgenic lines, indicating that this pathway is likely involved in the OsDOS-mediated delaying of leaf senescence. Furthermore, methyl JA treatments of both seeds and detached leaves from the RNAi and the overexpressing transgenic lines showed hyperand hyporesponses, respectively, consistent with the negative regulation of the JA pathway by OsDOS. Together, these results indicate that OsDOS is a novel nuclear protein that delays leaf senescence likely, at least in part, by integrating developmental cues to the JA pathway.

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“…The discovery and functional annotation of CREs is thus one of the immediate next steps toward global understanding of gene regulatory mechanisms in C. reinhardtii (Wang et al, 2009). However, there are less than one dozen CREs annotated in C. reinhardtii to date, even though many TFs have been collected and deposited in a number of databases (Wingender et al, 1996;Higo et al, 1999;Rombauts et al, 1999;PortalesCasamar et al, 2010). The correspondences between CREs and regulatory proteins remain largely unknown.…”

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confidence: 99%

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

Ding

2012

Plant Physiology

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Chlamydomonas reinhardtii is one of the most important microalgae model organisms and has been widely studied toward the understanding of chloroplast functions and various cellular processes. Further exploitation of C. reinhardtii as a model system to elucidate various molecular mechanisms and pathways requires systematic study of gene regulation. However, there is a general lack of genome-scale gene regulation study, such as global cis-regulatory element (CRE) identification, in C. reinhardtii. Recently, large-scale genomic data in microalgae species have become available, which enable the development of efficient computational methods to systematically identify CREs and characterize their roles in microalgae gene regulation. Here, we performed in silico CRE identification at the whole genome level in C. reinhardtii using a comparative genomics-based method. We predicted a large number of CREs in C. reinhardtii that are consistent with experimentally verified CREs. We also discovered that a large percentage of these CREs form combinations and have the potential to work together for coordinated gene regulation in C. reinhardtii. Multiple lines of evidence from literature, gene transcriptional profiles, and gene annotation resources support our prediction. The predicted CREs will serve, to our knowledge, as the first large-scale collection of CREs in C. reinhardtii to facilitate further experimental study of microalgae gene regulation. The accompanying software tool and the predictions in C. reinhardtii are also made available through a Web-accessible database (http://hulab.ucf.edu/research/projects/Microalgae/sdcre/motifcomb.html).

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PlantCARE, a plant cis-acting regulatory element database

Cited by 533 publications

References 10 publications

Structural and Functional Assays of AtTLP18.3 Identify Its Novel Acid Phosphatase Activity in Thylakoid Lumen

Structural and Functional Assays of AtTLP18.3 Identify Its Novel Acid Phosphatase Activity in Thylakoid Lumen

A Novel Nuclear-Localized CCCH-Type Zinc Finger Protein, OsDOS, Is Involved in Delaying Leaf Senescence in Rice

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

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