DIALIGN: multiple DNA and protein sequence alignment at BiBiServ

Morgenstern, Burkhard

doi:10.1093/nar/gkh373

Cited by 215 publications

(152 citation statements)

References 19 publications

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“…Placental-specific cDNA and also genomic DNA of C. frutescens and C. annuum encoding for CS were also sequenced. The sequence obtained was checked for homology (39).…”

Section: Purification Of Csmentioning

confidence: 99%

RETRACTED: Characterization of capsaicin synthase and identification of its gene ( csy1 ) for pungency factor capsaicin in pepper ( Capsicum sp.)

Prasad

Kumar

Gururaj

et al. 2006

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

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“…Placental-specific cDNA and also genomic DNA of C. frutescens and C. annuum encoding for CS were also sequenced. The sequence obtained was checked for homology (39).…”

Section: Purification Of Csmentioning

confidence: 99%

RETRACTED: Characterization of capsaicin synthase and identification of its gene ( csy1 ) for pungency factor capsaicin in pepper ( Capsicum sp.)

Prasad

Kumar

Gururaj

et al. 2006

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

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“…The sequence alignment between SlPPH and AtPPH (Fig. 3B) was performed using the program DIALIGN (http://bibiserv.techfak.uni-bielefeld.de/dialign/ submission.html; Morgenstern, 2004).…”

Section: Biocomputational Methods and Phylogenetic Analysismentioning

confidence: 99%

Different Mechanisms Are Responsible for Chlorophyll Dephytylation during Fruit Ripening and Leaf Senescence in Tomato

et al. 2014

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Chlorophyll breakdown occurs in different green plant tissues (e.g. during leaf senescence and in ripening fruits). For different plant species, the PHEOPHORBIDE A OXYGENASE (PAO)/phyllobilin pathway has been described to be the major chlorophyll catabolic pathway. In this pathway, pheophorbide (i.e. magnesium-and phytol-free chlorophyll) occurs as a core intermediate. Most of the enzymes involved in the PAO/phyllobilin pathway are known; however, the mechanism of dephytylation remains uncertain. During Arabidopsis (Arabidopsis thaliana) leaf senescence, phytol hydrolysis is catalyzed by PHEOPHYTINASE (PPH), which is specific for pheophytin (i.e. magnesium-free chlorophyll). By contrast, in fruits of different Citrus spp., chlorophyllase, hydrolyzing phytol from chlorophyll, was shown to be active. Here, we enlighten the process of chlorophyll breakdown in tomato (Solanum lycopersicum), both in leaves and fruits. We demonstrate the activity of the PAO/phyllobilin pathway and identify tomato PPH (SlPPH), which, like its Arabidopsis ortholog, was specifically active on pheophytin. SlPPH localized to chloroplasts and was transcriptionally up-regulated during leaf senescence and fruit ripening. SlPPH-silencing tomato lines were impaired in chlorophyll breakdown and accumulated pheophytin during leaf senescence. However, although pheophytin transiently accumulated in ripening fruits of SlPPH-silencing lines, ultimately these fruits were able to degrade chlorophyll like the wild type. We conclude that PPH is the core phytol-hydrolytic enzyme during leaf senescence in different plant species; however, fruit ripening involves other hydrolases, which are active in parallel to PPH or are the core hydrolases in fruits. These hydrolases remain unidentified, and we discuss the question of whether chlorophyllases might be involved.

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“…Bioinformatics-Multiple sequence alignments of proteins were computed using DIALIGN (29) and ClustalW (30). PAN3 proteins containing the PAM-2 motif were identified through a Basic Local Alignment Search Tool (BLAST) (31) at NCBI (www.ncbi.nlm.nih.gov/blast/) using the search option for short nearly exact matches.…”

Section: Methodsmentioning

confidence: 99%

Poly(A) Nuclease Interacts with the C-terminal Domain of Polyadenylate-binding Protein Domain from Poly(A)-binding Protein

Siddiqui

Mangus

Chang³

et al. 2007

Journal of Biological Chemistry

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The poly(A)-binding protein (PABP) is an essential protein found in all eukaryotes and is involved in an extensive range of cellular functions, including translation, mRNA metabolism, and mRNA export. Its C-terminal region contains a peptideinteracting PABC domain that recruits proteins containing a highly specific PAM-2 sequence motif to the messenger ribonucleoprotein complex. In humans, these proteins, including Paip1, Paip2, eRF3 (eukaryotic release factor 3), Ataxin-2, and Tob2, are all found to regulate translation through varying mechanisms. The following reports poly(A) nuclease (PAN) as a PABC-interacting partner in both yeast and humans. Their interaction is mediated by a PAM-2 motif identified within the PAN3 subunit. This site was identified in various fungal and animal species suggesting that the interaction is conserved throughout evolution. Our results indicate that PABP is directly involved in recruiting a deadenylase to the messenger ribonucleoprotein complex. This demonstrates a novel role for the PABC domain in mRNA metabolic processes and gives further insight into the function of PABP in mRNA maturation, export, and turnover.

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DIALIGN: multiple DNA and protein sequence alignment at BiBiServ

Cited by 215 publications

References 19 publications

RETRACTED: Characterization of capsaicin synthase and identification of its gene ( csy1 ) for pungency factor capsaicin in pepper ( Capsicum sp.)

RETRACTED: Characterization of capsaicin synthase and identification of its gene ( csy1 ) for pungency factor capsaicin in pepper ( Capsicum sp.)

Different Mechanisms Are Responsible for Chlorophyll Dephytylation during Fruit Ripening and Leaf Senescence in Tomato

Poly(A) Nuclease Interacts with the C-terminal Domain of Polyadenylate-binding Protein Domain from Poly(A)-binding Protein

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