PLACE: a database of plant cis-acting regulatory DNA elements

Higo, Kenichi; Ugawa, Yoshihiro; Iwamoto, Masao; Higo, Hiromi

doi:10.1093/nar/26.1.358

Cited by 280 publications

(191 citation statements)

References 8 publications

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“…In another study, similar altered responses in auxin signaling and enhanced responses to ABA were observed when OsWRKY72 was ectopically overexpressed in Arabidopsis . Scanning 1 kb of upstream promoter region from OsWRKY72 through the PLACe database (Higo et al 1998) shows an enrichment of ABRe-like elements. This suggests that this interaction of bZIP transcription factors with promoters from some wRKY gene promoters is crucial not only for ABA signaling but also for auxin signaling.…”

Section: Transcription Factors and Droughtmentioning

confidence: 99%

A systems biology perspective on the role of WRKY transcription factors in drought responses in plants

Tripathi

Rabara

Rushton

2013

Planta

202

130

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Section: Transcription Factors and Droughtmentioning

confidence: 99%

A systems biology perspective on the role of WRKY transcription factors in drought responses in plants

Tripathi

Rabara

Rushton

2013

Planta

202

130

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“…Then, these sequences were subjected to Plant cis-acting Regulatory DNA Elements (PLACE) database (http://www.dna.affrc.go.jp/PLACE/signalscan.html) [26] to identify cis-regulatory elements and those motifs with clearly more than 200 copies were collected for functional annotation analysis.…”

Section: Cis-regulatory Element Analysis Of Mtexp Genesmentioning

confidence: 99%

In silicoidentification, phylogeny and expression analysis of expansin superfamily inMedicago truncatula

Liu

Zhang

et al. 2015

Biotechnology & Biotechnological Equipment

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Expansins are important components of plant cell walls, which are involved in the process of cell wall loosening under low extracellular pH. By using a combinational method for homology search and protein domain analysis, a total of 42 expansin genes were identified from Medicago truncatula genome in this study. They were divided into four families, based on sequence alignment and phylogenetic analysis. Gene duplication events were identified in the expansins superfamily, especially in the extension of a-expansin family. By analysis of RNA-sequencing data from National Center for Biotechnology Information, the expansin (EXP) genes expressed during tissues development were characterized. Meanwhile, lots of cis-acting regulatory DNA elements in the EXP superfamily were identified, which were mainly related to plant growth and development processes. The results presented in this study are expected to facilitate further research works on this gene superfamily and provide new insights about the molecular mechanisms of expansins in M. truncatula.

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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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PLACE: a database of plant cis-acting regulatory DNA elements

Cited by 280 publications

References 8 publications

A systems biology perspective on the role of WRKY transcription factors in drought responses in plants

A systems biology perspective on the role of WRKY transcription factors in drought responses in plants

In silicoidentification, phylogeny and expression analysis of expansin superfamily inMedicago truncatula

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

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