In silico identification, characterization and expression profile of WUSCHEL-related homeobox (WOX) gene family in Vanilla planifolia
DOI:
https://doi.org/10.14719/pst.2020.7.2.722Keywords:
Vanilla planifolia, WUSCHEL, WOX genes, Gene family characterization, Expression analysisAbstract
Vanilla planifolia is an economically important orchid, which is being commercially exploited by the food industry for the highly valued secondary metabolite vanillin. WUSCHEL-related homeobox (WOX) gene family encodes for WUSCHEL-related homeobox (WOX) transcription factors that participate in embryogenesis, organogenesis and florigenesis and in diverse plant developmental processes as well. In the present study, we analysed V. planifolia transcriptome and identified 6 WOX (VpWOX) transcripts, that encode putative WOX (VpWOX) transcription factor proteins. Domain analysis was done which indicates the presence of helix-loop-helix-turn-helix which is identifying feature of WOX gene family proteins. We executed phylogenetic clustering for the VpWOX proteins with their counterpart from the model plant Arabidopsis thaliana (AtWOX) and other closely related orchid species, Phalaenopsis equestris (PeWOX), Dendrobium catenatum (DcWOX) and Apostasia shenzhenica (AsWOX) and established their clade specific grouping. Spatio-temporal expression profile for VpWOX genes was analysed for different plant developmental stages which shows that VpWOX13 is expressing uniformly in all the developmental stages whereas, other genes have tissue specific expression. Based on gene expression patterns, we selected four VpWOX proteins and carried out secondary and tertiary structural analysis which indicates the presence of alpha helix and beta turn in the protein structure. The present study provides basic understanding of the functioning of WOX gene family in V. planifolia and paves the path for functional characterization of selected VpWOX genes in planta and in heterologous system in future for commercial utilization.
Downloads
Download data is not yet available.
References
1. Laux T, Mayer KF, Berger J, Jurgens G. The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis. Development. 1996;122(1):87-96. https://doi.org/10.1371/journal.pone.0038161
2. Zuo J, Niu QW, Frugis G, Chua NH. The WUSCHEL gene promotes vegetative?to?embryonic transition in Arabidopsis. The Plant Journal. 2002;30(3):349-59. https://doi.org/10.1046/j.1365-313X.2002.01289.x
3. Arroyo-Herrera A, Gonzalez AK, Moo RC, Quiroz-Figueroa FR, Loyola-Vargas VM, Rodriguez-Zapata LC, et al. Expression of WUSCHEL in Coffea canephora causes ectopic morphogenesis and increases somatic embryogenesis. Plant Cell, Tissue and Organ Culture. 2008;94(2):171-80. https://doi.org/10.1007/s11240-008-9401-1
4. Bouchabke-Coussa O, Obellianne M, Linderme D, Montes E, Maia-Grondard A, Vilaine F, et al. WUSCHEL overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro. Plant Cell Reports. 2013;32(5):675-86. https://doi.org/10.1007/s00299-013-1402-9
5. Kundu A. Vanillin biosynthetic pathways in plants. Planta. 2017;245(6):1069-78. https://doi.org/10.1007/s00425-017-2684-x
6. Gehring WJ, Affolter M, Bürglin T. Homeodomain proteins. Annual Review of Biochemistry. 1994;63(1):487-526. https://doi.org/10.1146/annurev.bi.63.070194.002415
7. Kamiya N, Nagasaki H, Morikami A, Sato Y, Matsuoka M. Isolation and characterization of a rice WUSCHEL?type homeobox gene that is specifically expressed in the central cells of a quiescent center in the root apical meristem. The Plant Journal. 2003;35(4):429-41. https://doi.org/10.1046/j.1365-313X.2003.01816.x
8. van der Graaff E, Laux T, Rensing SA. The WUS homeobox-containing (WOX) protein family. Genome Biology. 2009; 10(12): 248. https://doi.org/10.1186/gb-2009-10-12-248
9. Lian G, Ding Z, Wang Q, Zhang D, Xu J. Origins and evolution of WUSCHEL-related homeobox protein family in plant kingdom. The Scientific World Journal. 2014;2014. https://doi.org/10.1155/2014/534140
10. Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. Annals of Botany. 2014;114(7): 1545-53. https://doi.org/10.1093/aob/mcu123
11. Ramkumar TR, Kanchan M, Upadhyay SK, Sembi JK. Identification and characterization of WUSCHEL-related homeobox (WOX) gene family in economically important orchid species Phalaenopsis equestris and Dendrobium catenatum. Plant Gene. 2018;14:37-45. https://doi.org/10.1016/j.plgene.2018.04.004
12. Ramkumar TR, Kanchan M, Sembi JK. Genome wide characterization of WUSCHEL-related homeobox (WOX) gene family in Apostasia shenzhenica, a Primeval Orchid. Plant Science Today. 2020;7(2):164-171. https://doi.org/10.14719/pst.2020.7.2.703
13. Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC. Orchidstra 2.0—a transcriptomics resource for the orchid family. Plant and Cell Physiology. 2017;58(1):e9-. https://doi.org/10.1093/pcp/pcw220
14. Sigrist CJ, De Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I. New and continuing developments at PROSITE. Nucleic Acids Research. 2012;41(D1):D344-7. https://doi.org/10.1093/nar/gks1067
15. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research. 1988;16(22):10881-90. https://doi.org/10.1093/nar/16.22.10881
16. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research. 2009;37(suppl_2):W202-8. https://doi.org/10.1093/nar/gkp335
17. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, et al. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook. 2005:571-607. https://doi.org/10.1385/1-59259-890-0:571
18. Yu CS, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics. 2006;64(3):643-51. https://doi.org/10.1002/prot.21018
19. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, et al. WoLF PSORT: protein localization predictor. Nucleic Acids Research. 2007;35(suppl_2):W585-7. https://doi.org/10.1093/nar/gkm259
20. Petersen TN, Brunak S, Von Heijne G, Nielsen H. Signal P 4.0: discriminating signal peptides from transmembrane regions. Nature Methods. 2011;8(10):785. https://doi.org/10.1038/nmeth.1701
21. Krogh A, Larsson B, Von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology. 2001;305(3):567-80. https://doi.org/10.1006/jmbi.2000.4315
22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 2016;33(7):1870. https://doi.org/10.1093/molbev/msw054
23. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 2004; 32(5):1792-97. https://doi.org/10.1093/nar/gkh340
24. Pearson WR. An introduction to sequence similarity (“homology”) searching. Current Protocols in Bioinformatics. 2013;42:3-1. https://doi.org/10.1002/0471250953.bi0301s42
25. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods. 2008;5(7):621. https://doi.org/10.1038/nmeth.1226
26. Seo J, Gordish-Dressman H, Hoffman EP. An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics. 2006;22(7):808-14. https://doi.org/10.1093/bioinformatics/btk052
27. Sapay N, Guermeur Y, Deléage G. Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier. BMC bioinformatics. 2006;7(1):255. https://dx.doi.org/10.1186%2F1471-2105-7-255
28. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nature Methods. 2015;12(1):7. https://doi.org/10.1038/nmeth.3213
29. Rahman ZU, Azam SM, Liu Y, Yan C, Ali H, Zhao L, et al. Expression profiles of Wuschel-related homeobox gene family in pineapple (Ananas comosus L). Tropical Plant Biology. 2017; 4(10):204-15. https://doi.org/10.1007/s12042-017-9192-9
30. Deveaux Y, Toffano-Nioche C, Claisse G, Thareau V, Morin H, Laufs P, et al. Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis. BMC Evolutionary Biology. 2008;8(1):291. https://doi.org/10.1186/1471-2148-8-291
31. Romera?Branchat M, Ripoll JJ, Yanofsky MF, Pelaz S. The WOX 13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit. The Plant Journal. 2013;73(1):37-49. https://doi.org/10.1111/tpj.12010
32. Sakakibara K, Reisewitz P, Aoyama T, Friedrich T, Ando S, Sato Y, et al. WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens. Development. 2014;141(8):1660-70. https://doi.org/10.1242/dev.097444
33. Colombo L, Battaglia R, Kater MM. Arabidopsis ovule development and its evolutionary conservation. Trends in Plant Science. 2008;13(8):444-50. https://doi.org/10.1016/j.tplants.2008.04.011
34. Ikeda M, Mitsuda N, Ohme-Takagi M. Arabidopsis WUSCHEL is a bifunctional transcription factor that acts as a repressor in stem cell regulation and as an activator in floral patterning. The Plant Cell. 2009;21(11):3493-505. https://doi.org/10.1105/tpc.109.069997
35. Silva AT, Paiva LV, Andrade AC, Barduche D. Identification of expressed sequences in the coffee genome potentially associated with somatic embryogenesis. Genetics and Molecular Biology Research. 2013;12:1698-709. https://doi.org/10.4238/2013.May.21.1
36. Breuninger H, Rikirsch E, Hermann M, Ueda M, Laux T. Differential expression of WOX genes mediates apical-basal axis formation in the Arabidopsis embryo. Developmental cell. 2008;14(6):867-76. https://doi.org/10.1016/j.devcel.2008.03.008
37. Hu X, Xu L. Transcription factors WOX11/12 directly activate WOX5/7 to promote root primordia initiation and organogenesis. Plant Physiology. 2016;172:2363-73. https://doi.org/10.1104/pp.16.01067
38. Jiang W, Zhou S, Zhang Q, Song H, Zhou DX, Zhao Y. Transcriptional regulatory network of WOX11 is involved in the control of crown root development, cytokinin signals and redox in rice. Journal of Experimental Botany. 2017;68:2787-98. https://doi.org/10.1093/jxb/erx153
39. Zhao Y, Hu Y, Dai M, Huang L, Zhou DX. The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice. The Plant Cell. 2009;21:736-48. https://doi.org/10.1105/tpc.108.061655
40. Cheng S, Zhou DX, Zhao Y. WUSCHEL-related homeobox gene WOX11 increases rice drought resistance by controlling root hair formation and root system development. Plant Signaling & Behavior. 2016;11(2):e1130198. https://doi.org/10.1080/15592324.2015.1130198
41. Auffinger P, Grover N, Westhof E. Metal ion binding to RNA. Metal Ions in Life Science. 2011;9(1). https://doi.org/10.1039/9781849732512-00001
2. Zuo J, Niu QW, Frugis G, Chua NH. The WUSCHEL gene promotes vegetative?to?embryonic transition in Arabidopsis. The Plant Journal. 2002;30(3):349-59. https://doi.org/10.1046/j.1365-313X.2002.01289.x
3. Arroyo-Herrera A, Gonzalez AK, Moo RC, Quiroz-Figueroa FR, Loyola-Vargas VM, Rodriguez-Zapata LC, et al. Expression of WUSCHEL in Coffea canephora causes ectopic morphogenesis and increases somatic embryogenesis. Plant Cell, Tissue and Organ Culture. 2008;94(2):171-80. https://doi.org/10.1007/s11240-008-9401-1
4. Bouchabke-Coussa O, Obellianne M, Linderme D, Montes E, Maia-Grondard A, Vilaine F, et al. WUSCHEL overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro. Plant Cell Reports. 2013;32(5):675-86. https://doi.org/10.1007/s00299-013-1402-9
5. Kundu A. Vanillin biosynthetic pathways in plants. Planta. 2017;245(6):1069-78. https://doi.org/10.1007/s00425-017-2684-x
6. Gehring WJ, Affolter M, Bürglin T. Homeodomain proteins. Annual Review of Biochemistry. 1994;63(1):487-526. https://doi.org/10.1146/annurev.bi.63.070194.002415
7. Kamiya N, Nagasaki H, Morikami A, Sato Y, Matsuoka M. Isolation and characterization of a rice WUSCHEL?type homeobox gene that is specifically expressed in the central cells of a quiescent center in the root apical meristem. The Plant Journal. 2003;35(4):429-41. https://doi.org/10.1046/j.1365-313X.2003.01816.x
8. van der Graaff E, Laux T, Rensing SA. The WUS homeobox-containing (WOX) protein family. Genome Biology. 2009; 10(12): 248. https://doi.org/10.1186/gb-2009-10-12-248
9. Lian G, Ding Z, Wang Q, Zhang D, Xu J. Origins and evolution of WUSCHEL-related homeobox protein family in plant kingdom. The Scientific World Journal. 2014;2014. https://doi.org/10.1155/2014/534140
10. Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. Annals of Botany. 2014;114(7): 1545-53. https://doi.org/10.1093/aob/mcu123
11. Ramkumar TR, Kanchan M, Upadhyay SK, Sembi JK. Identification and characterization of WUSCHEL-related homeobox (WOX) gene family in economically important orchid species Phalaenopsis equestris and Dendrobium catenatum. Plant Gene. 2018;14:37-45. https://doi.org/10.1016/j.plgene.2018.04.004
12. Ramkumar TR, Kanchan M, Sembi JK. Genome wide characterization of WUSCHEL-related homeobox (WOX) gene family in Apostasia shenzhenica, a Primeval Orchid. Plant Science Today. 2020;7(2):164-171. https://doi.org/10.14719/pst.2020.7.2.703
13. Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC. Orchidstra 2.0—a transcriptomics resource for the orchid family. Plant and Cell Physiology. 2017;58(1):e9-. https://doi.org/10.1093/pcp/pcw220
14. Sigrist CJ, De Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I. New and continuing developments at PROSITE. Nucleic Acids Research. 2012;41(D1):D344-7. https://doi.org/10.1093/nar/gks1067
15. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research. 1988;16(22):10881-90. https://doi.org/10.1093/nar/16.22.10881
16. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research. 2009;37(suppl_2):W202-8. https://doi.org/10.1093/nar/gkp335
17. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, et al. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook. 2005:571-607. https://doi.org/10.1385/1-59259-890-0:571
18. Yu CS, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics. 2006;64(3):643-51. https://doi.org/10.1002/prot.21018
19. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, et al. WoLF PSORT: protein localization predictor. Nucleic Acids Research. 2007;35(suppl_2):W585-7. https://doi.org/10.1093/nar/gkm259
20. Petersen TN, Brunak S, Von Heijne G, Nielsen H. Signal P 4.0: discriminating signal peptides from transmembrane regions. Nature Methods. 2011;8(10):785. https://doi.org/10.1038/nmeth.1701
21. Krogh A, Larsson B, Von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology. 2001;305(3):567-80. https://doi.org/10.1006/jmbi.2000.4315
22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 2016;33(7):1870. https://doi.org/10.1093/molbev/msw054
23. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research. 2004; 32(5):1792-97. https://doi.org/10.1093/nar/gkh340
24. Pearson WR. An introduction to sequence similarity (“homology”) searching. Current Protocols in Bioinformatics. 2013;42:3-1. https://doi.org/10.1002/0471250953.bi0301s42
25. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods. 2008;5(7):621. https://doi.org/10.1038/nmeth.1226
26. Seo J, Gordish-Dressman H, Hoffman EP. An interactive power analysis tool for microarray hypothesis testing and generation. Bioinformatics. 2006;22(7):808-14. https://doi.org/10.1093/bioinformatics/btk052
27. Sapay N, Guermeur Y, Deléage G. Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier. BMC bioinformatics. 2006;7(1):255. https://dx.doi.org/10.1186%2F1471-2105-7-255
28. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nature Methods. 2015;12(1):7. https://doi.org/10.1038/nmeth.3213
29. Rahman ZU, Azam SM, Liu Y, Yan C, Ali H, Zhao L, et al. Expression profiles of Wuschel-related homeobox gene family in pineapple (Ananas comosus L). Tropical Plant Biology. 2017; 4(10):204-15. https://doi.org/10.1007/s12042-017-9192-9
30. Deveaux Y, Toffano-Nioche C, Claisse G, Thareau V, Morin H, Laufs P, et al. Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis. BMC Evolutionary Biology. 2008;8(1):291. https://doi.org/10.1186/1471-2148-8-291
31. Romera?Branchat M, Ripoll JJ, Yanofsky MF, Pelaz S. The WOX 13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit. The Plant Journal. 2013;73(1):37-49. https://doi.org/10.1111/tpj.12010
32. Sakakibara K, Reisewitz P, Aoyama T, Friedrich T, Ando S, Sato Y, et al. WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens. Development. 2014;141(8):1660-70. https://doi.org/10.1242/dev.097444
33. Colombo L, Battaglia R, Kater MM. Arabidopsis ovule development and its evolutionary conservation. Trends in Plant Science. 2008;13(8):444-50. https://doi.org/10.1016/j.tplants.2008.04.011
34. Ikeda M, Mitsuda N, Ohme-Takagi M. Arabidopsis WUSCHEL is a bifunctional transcription factor that acts as a repressor in stem cell regulation and as an activator in floral patterning. The Plant Cell. 2009;21(11):3493-505. https://doi.org/10.1105/tpc.109.069997
35. Silva AT, Paiva LV, Andrade AC, Barduche D. Identification of expressed sequences in the coffee genome potentially associated with somatic embryogenesis. Genetics and Molecular Biology Research. 2013;12:1698-709. https://doi.org/10.4238/2013.May.21.1
36. Breuninger H, Rikirsch E, Hermann M, Ueda M, Laux T. Differential expression of WOX genes mediates apical-basal axis formation in the Arabidopsis embryo. Developmental cell. 2008;14(6):867-76. https://doi.org/10.1016/j.devcel.2008.03.008
37. Hu X, Xu L. Transcription factors WOX11/12 directly activate WOX5/7 to promote root primordia initiation and organogenesis. Plant Physiology. 2016;172:2363-73. https://doi.org/10.1104/pp.16.01067
38. Jiang W, Zhou S, Zhang Q, Song H, Zhou DX, Zhao Y. Transcriptional regulatory network of WOX11 is involved in the control of crown root development, cytokinin signals and redox in rice. Journal of Experimental Botany. 2017;68:2787-98. https://doi.org/10.1093/jxb/erx153
39. Zhao Y, Hu Y, Dai M, Huang L, Zhou DX. The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice. The Plant Cell. 2009;21:736-48. https://doi.org/10.1105/tpc.108.061655
40. Cheng S, Zhou DX, Zhao Y. WUSCHEL-related homeobox gene WOX11 increases rice drought resistance by controlling root hair formation and root system development. Plant Signaling & Behavior. 2016;11(2):e1130198. https://doi.org/10.1080/15592324.2015.1130198
41. Auffinger P, Grover N, Westhof E. Metal ion binding to RNA. Metal Ions in Life Science. 2011;9(1). https://doi.org/10.1039/9781849732512-00001
Downloads
Published
18-04-2020
How to Cite
1.
Victorathisayam T, Kanchan M, Himani `, Suriyanarayanan TR, Sembi JK, Ramkumar TR. In silico identification, characterization and expression profile of WUSCHEL-related homeobox (WOX) gene family in Vanilla planifolia. Plant Sci. Today [Internet]. 2020 Apr. 18 [cited 2024 May 10];7(2):206-13. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/722
Issue
Section
Research Articles
License
Copyright and Licence details of published articles
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
Open Access Policy
Plant Science Today is an open access journal. There is no registration required to read any article. All published articles are distributed under the terms of the Creative Commons Attribution License (CC Attribution 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited (https://creativecommons.org/licenses/by/4.0/). Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
