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In silico study for diversing the molecular pathway of pigment formation: an alternative to manual coloring in cotton fibers.

Ahad A, Ahmad A, Din SU, Rao AQ, Shahid AA, Husnain T - Front Plant Sci (2015)

Bottom Line: Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols.Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK.It will help in color manipulations in different plant species.

View Article: PubMed Central - PubMed

Affiliation: Center of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.

ABSTRACT
Diversity of colors in flowers and fruits is largely due to anthocyanin pigments. The flavonoid/anthocyanin pathway has been most extensively studied. Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols. The substrate specificity of the DFR was found to play a crucial role in determination of type of anthocyanidins. Altering the flavonoid/anthocyanin pathway through genetic engineering to develop color of our own choice is an exciting subject of future research. In the present study, comparison among four DFR genes (Gossypium hirsutum, Iris × hollandica, Ang. DFRI and DFRII), sequence alignment for homology as well as protein modeling and docking is demonstrated. Estimation of catalytic sites, prediction of substrate preference and protein docking were the key features of this article. For specific substrate uptake, a proline rich region and positions 12 plus 26 along with other positions emphasizing the 26-amino acid residue region (132-157) was tested. Results showed that proline rich region position 12, 26, and 132-157 plays an important role in selective attachment of DFRs with respective substrates. Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK. Protein docking data showed that amino acid residues in above mentioned positions were just involved in attachment of DFR with substrate and had no role in specific substrate uptake. Advanced bioinformatics analysis has revealed that all above mentioned positions have role in substrate attachment. For substrate specificity, other residues region is involved. It will help in color manipulations in different plant species.

No MeSH data available.


Multiple sequence alignment of dihydroflavanol 4-reductase, consensus sequences of different plant species (Rosa chinensis, Vaccinium macrocarpon, Gerbera hybrid, Petunia × hybrid, Ang. DFRI, Ang. DFRII, Gossypium hirsutum, Iris × hollandica, and Ampelopsis grossedentata) were achieved by using CLC Genomics Workbench 8. The colored bars at the bottom are representing the conservation Percentage.
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Figure 2: Multiple sequence alignment of dihydroflavanol 4-reductase, consensus sequences of different plant species (Rosa chinensis, Vaccinium macrocarpon, Gerbera hybrid, Petunia × hybrid, Ang. DFRI, Ang. DFRII, Gossypium hirsutum, Iris × hollandica, and Ampelopsis grossedentata) were achieved by using CLC Genomics Workbench 8. The colored bars at the bottom are representing the conservation Percentage.

Mentions: For comparison, at position 12 and 26, DFR sequences were aligned by using the CLC Genomics Workbench 8 as mentioned earlier. From sequence alignment results it was evaluated that at position 12, Ang. DFRI, Ang. DFRII, Gossypium hirsutum DFR, and Iris × hollandica DFR have proline, serine, proline and glycine respectively. This result showed same residue (proline) in both Gossypium hirsutum and Angelonia DFR I whereas, Angelonia DFRII and Iris × hollandica DFR had serine and glycine which were functionally similar residues (Figure 1). In present study, the sequence alignment showed proline at 12 position in Gossypium hirsutum from which it is hypothesized that it would reduce dihydrokaempferol. Whereas, this particular region is absent in both Iris × hollandica and Ang.II DFRs, resulting in delphinidin accumulation which is responsible for production of blue color (Figure 2). For further confirmation DFRs from five more species along with these four plant species were carried out to evaluate results. However, with respect to Ang. DFRI, sequence alignment of other five species (Rosa chinensis, Vaccinium macrocarpon, Gerbera hybrid, Petunia × hybrida, and Ampelopsis grossedentata) showed the deletion of proline rich region and thus unable to reduce DHK.


In silico study for diversing the molecular pathway of pigment formation: an alternative to manual coloring in cotton fibers.

Ahad A, Ahmad A, Din SU, Rao AQ, Shahid AA, Husnain T - Front Plant Sci (2015)

Multiple sequence alignment of dihydroflavanol 4-reductase, consensus sequences of different plant species (Rosa chinensis, Vaccinium macrocarpon, Gerbera hybrid, Petunia × hybrid, Ang. DFRI, Ang. DFRII, Gossypium hirsutum, Iris × hollandica, and Ampelopsis grossedentata) were achieved by using CLC Genomics Workbench 8. The colored bars at the bottom are representing the conservation Percentage.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584984&req=5

Figure 2: Multiple sequence alignment of dihydroflavanol 4-reductase, consensus sequences of different plant species (Rosa chinensis, Vaccinium macrocarpon, Gerbera hybrid, Petunia × hybrid, Ang. DFRI, Ang. DFRII, Gossypium hirsutum, Iris × hollandica, and Ampelopsis grossedentata) were achieved by using CLC Genomics Workbench 8. The colored bars at the bottom are representing the conservation Percentage.
Mentions: For comparison, at position 12 and 26, DFR sequences were aligned by using the CLC Genomics Workbench 8 as mentioned earlier. From sequence alignment results it was evaluated that at position 12, Ang. DFRI, Ang. DFRII, Gossypium hirsutum DFR, and Iris × hollandica DFR have proline, serine, proline and glycine respectively. This result showed same residue (proline) in both Gossypium hirsutum and Angelonia DFR I whereas, Angelonia DFRII and Iris × hollandica DFR had serine and glycine which were functionally similar residues (Figure 1). In present study, the sequence alignment showed proline at 12 position in Gossypium hirsutum from which it is hypothesized that it would reduce dihydrokaempferol. Whereas, this particular region is absent in both Iris × hollandica and Ang.II DFRs, resulting in delphinidin accumulation which is responsible for production of blue color (Figure 2). For further confirmation DFRs from five more species along with these four plant species were carried out to evaluate results. However, with respect to Ang. DFRI, sequence alignment of other five species (Rosa chinensis, Vaccinium macrocarpon, Gerbera hybrid, Petunia × hybrida, and Ampelopsis grossedentata) showed the deletion of proline rich region and thus unable to reduce DHK.

Bottom Line: Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols.Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK.It will help in color manipulations in different plant species.

View Article: PubMed Central - PubMed

Affiliation: Center of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.

ABSTRACT
Diversity of colors in flowers and fruits is largely due to anthocyanin pigments. The flavonoid/anthocyanin pathway has been most extensively studied. Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols. The substrate specificity of the DFR was found to play a crucial role in determination of type of anthocyanidins. Altering the flavonoid/anthocyanin pathway through genetic engineering to develop color of our own choice is an exciting subject of future research. In the present study, comparison among four DFR genes (Gossypium hirsutum, Iris × hollandica, Ang. DFRI and DFRII), sequence alignment for homology as well as protein modeling and docking is demonstrated. Estimation of catalytic sites, prediction of substrate preference and protein docking were the key features of this article. For specific substrate uptake, a proline rich region and positions 12 plus 26 along with other positions emphasizing the 26-amino acid residue region (132-157) was tested. Results showed that proline rich region position 12, 26, and 132-157 plays an important role in selective attachment of DFRs with respective substrates. Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK. Protein docking data showed that amino acid residues in above mentioned positions were just involved in attachment of DFR with substrate and had no role in specific substrate uptake. Advanced bioinformatics analysis has revealed that all above mentioned positions have role in substrate attachment. For substrate specificity, other residues region is involved. It will help in color manipulations in different plant species.

No MeSH data available.