Predicting the Function of 4-Coumarate:CoA Ligase (LJ4CL1) in Lonicera japonica
Abstract
:1. Introduction
2. Results and Discussion
2.1. Global Phylogeny and Duplication of AMP-Binding Proteins
2.2. Global Phylogeny and Duplication of GEICIRG-Containing Proteins
2.3. Expression of GEICIRG-Containing Proteins in L. japonica Flowers
2.4. Substrate-Binding Diversity in the Expressed GEICIRG-Containing Proteins in L. japonica
3. Experimental Section
3.1. Classification of AMP-Dependent Synthetase/Ligase Sequences and GEICIRG-Motif Proteins
3.2. Phylogeny of AMP-Dependent Synthetase/Ligase Sequences and GEICIRG-Motif Proteins
3.3. Indentification of Orthologs and Paralogs
3.4. Gene Expression Analyses
3.5. Protein Structure and Binding Site Prediction
3.6. LC-MS Analysis of L. japonica Flowers
3.7. Expression of 4CL Protein in E.coli and Enzyme Activity Assay
4. Conclusions
Supplementary Information
ijms-15-02386-s001.pdfAcknowledgments
Conflicts of Interest
References
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Kingdom Group | Class | Clusters * | Number of copies | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Species | 1 | 1-1 | 1-2 | 1-3 | 1-4 | 2 | 2-1 | 2-2 | 2-3 | 2-4 | 3 | Total | |||
Animal | Culex quinquefasciatus | 39 | 5 | 5 | 27 | 2 | 6 | 1 | 4 | 1 | 0 | 1 | 46 | ||
Bacteria | Escherichia coli | 5 | 0 | 3 | 2 | 0 | 3 | 0 | 2 | 1 | 0 | 2 | 10 | ||
Fungus | Penicillium marneffei | 20 | 3 | 3 | 12 | 2 | 25 | 3 | 7 | 15 | 0 | 5 | 50 | ||
Aspergillus nidulans | 32 | 2 | 8 | 17 | 5 | 28 | 3 | 5 | 19 | 1 | 1 | 61 | |||
Plant | Algae | Chlamydomonas reinhardtii | 18 | 11 | 2 | 0 | 5 | 9 | 0 | 8 | 0 | 1 | 0 | 27 | |
Bryophyte | Physcomitrella patens | 43 | 8 | 16 | 14 | 5 | 2 | 0 | 0 | 1 | 1 | 0 | 45 | ||
Pteridophyta | Selaginella moellendorffii | 70 | 15 | 26 | 26 | 3 | 14 | 3 | 9 | 2 | 0 | 0 | 84 | ||
Gymnospermae | Pinus taeda | 4 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | ||
Larix gmelinii | 18 | 0 | 0 | 18 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 18 | |||
Pseudotsuga menziesii | 17 | 0 | 0 | 17 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 17 | |||
Angiospermae | Dicotyledoneae | Glycine max | 99 | 30 | 29 | 35 | 5 | 12 | 5 | 6 | 1 | 0 | 0 | 111 | |
Populus trichocarpa | 71 | 21 | 24 | 23 | 3 | 8 | 3 | 4 | 1 | 0 | 0 | 79 | |||
Arabidopsis thaliana | 48 | 13 | 17 | 16 | 2 | 6 | 0 | 5 | 1 | 0 | 0 | 54 | |||
Arabidopsis lyrata | 146 | 24 | 0 | 122 | 0 | 25 | 8 | 15 | 2 | 0 | 1 | 172 | |||
Vitis vinifera | 34 | 8 | 9 | 14 | 3 | 6 | 1 | 4 | 1 | 0 | 0 | 40 | |||
Lonicera japonica | 103 | 43 | 36 | 17 | 7 | 14 | 0 | 12 | 2 | 0 | 0 | 117 | |||
Lonicera japonica var. chinensis | 73 | 33 | 20 | 16 | 4 | 12 | 0 | 10 | 2 | 0 | 1 | 86 | |||
Monocotyledoneae | Zea mays | 82 | 23 | 21 | 35 | 3 | 15 | 3 | 9 | 3 | 0 | 0 | 97 | ||
Sorghum bicolor | 48 | 16 | 13 | 17 | 2 | 10 | 3 | 6 | 1 | 0 | 0 | 58 | |||
Oryza sativa | 60 | 31 | 12 | 16 | 1 | 16 | 3 | 9 | 4 | 0 | 0 | 76 | |||
Total | 1252 |
Clusters * | Number of copies | Total | Genome size | Reference | |||||
---|---|---|---|---|---|---|---|---|---|
ACS | AAE | 4CL | ACS | ||||||
Species | 1 | 2 | 3 | 4 | M | ||||
Gymnospermae | Pinus pinaster | 0 | 0 | 1 | 0 | 1 | |||
Algae | Chlamydomonas reinhardtii | 2 | 0 | 0 | 1 | 3 | |||
Bryophyte | Physcomitrella patens | 0 | 3 | 12 | 0 | 15 | |||
Pteridophyta | Selaginella moellendorffii | 3 | 2 | 5 | 6 | 16 | |||
Angiospermae | Dicotyledoneae | Glycine max | 3 | 7 | 10 | 4 | 24 | 1100 | [33] |
Populus trichocarpa | 5 | 1 | 6 | 2 | 14 | 485 | [34] | ||
Arabidopsis thaliana | 2 | 1 | 7 | 5 | 15 | 135 | [35] | ||
Vitis vinifera | 2 | 2 | 3 | 2 | 9 | 505 | [36] | ||
Lonicera japonica | 5 | 4 | 1 | 5 | 15 | ||||
Lonicera japonica var. chinensis | 4 | 2 | 2 | 3 | 11 | ~800 | Our group | ||
Monocotyledoneae | Zea mays | 3 | 0 | 12 | 8 | 23 | 2300 | [37] | |
Sorghum bicolor | 2 | 1 | 8 | 4 | 15 | 730 | [38] | ||
Oryza sativa | 6 | 0 | 7 | 10 | 23 | 467 | [39] | ||
Total | 37 | 23 | 74 | 50 | 184 |
Cluster * | Varieties | Lonicera japonica | Lonicera japonica var. chinensis | Total |
---|---|---|---|---|
Copy and RPKM | ||||
1 | Number of copies | 5 | 4 | 9 |
RPKM | 320.4257 | 171.5426 | 491.9683 | |
2 | Number of copies | 4 | 2 | 6 |
RPKM | 250.9583 | 306.7299 | 557.6882 | |
3 | Number of copies | 1 | 2 | 3 |
RPKM | 50.3633 | 234.6021 | 284.9654 | |
4 | Number of copies | 5 | 3 | 8 |
RPKM | 292.3302 | 236.8353 | 529.1655 |
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Yuan, Y.; Yu, S.; Yu, J.; Zhan, Z.; Li, M.; Liu, G.; Wang, X.; Huang, L. Predicting the Function of 4-Coumarate:CoA Ligase (LJ4CL1) in Lonicera japonica. Int. J. Mol. Sci. 2014, 15, 2386-2399. https://doi.org/10.3390/ijms15022386
Yuan Y, Yu S, Yu J, Zhan Z, Li M, Liu G, Wang X, Huang L. Predicting the Function of 4-Coumarate:CoA Ligase (LJ4CL1) in Lonicera japonica. International Journal of Molecular Sciences. 2014; 15(2):2386-2399. https://doi.org/10.3390/ijms15022386
Chicago/Turabian StyleYuan, Yuan, Shulin Yu, Jun Yu, Zhilai Zhan, Minhui Li, Guiming Liu, Xumin Wang, and Luqi Huang. 2014. "Predicting the Function of 4-Coumarate:CoA Ligase (LJ4CL1) in Lonicera japonica" International Journal of Molecular Sciences 15, no. 2: 2386-2399. https://doi.org/10.3390/ijms15022386