Characterisation of actin depolymerising factor promoter (pTZPaADF) from Plectranthus amboinicus Lour (Spreng) using Arabidopsis thaliana (L.) Heynh as an internal control

S. M. Evangelene Christy; K. Aravind; V. Deepika; E. Steffi Selvarani; V. Arun

doi:10.7324/JABB.2023.144145

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Abstract

Plant genetic engineering heavily relies on transgenic technology. For the development of an effective vector system for genetic transformation application well-characterized promoter is crucial. Currently, available promoters are either viral or bacterial origin and hence it is necessary to isolate and analyze additional constitutive promoters of non-viral origin. Plant actin depolymerizing factors (ADFs) have diverse metabolic characteristics however, the majority of biological functions are yet unknown. In this study, we attempted to identify the promoter region of ADF from Plectranthus amboinicus using Arabidopsis thaliana as an internal control by thermal asymmetric interlaced polymerase chain reaction (TAIL PCR). Three heterologous gene-specific primers were designed to isolate the promoter region and the sequences were then examined in silico to check for the presence of minimal promoter elements. Our findings suggested that the TAIL PCR using specific primers is an efficient method for plant promoter isolation. The clone (pTZPaADF) carrying the putative promoter sequence was verified by comparing it with the results obtained for A. thaliana. Alignment of the putative promoter sequences with Arabidopsis revealed the presence of numerous conserved and shared RNA polymerase binding sites. In silico analysis revealed that there were several putative motifs including the TATA and the CAAT boxes. In addition, many other putative cis-acting regulatory elements that may regulate gene expression were also found. Based on the analysis the isolated putative promoter, pTZPaADF, could be employed in driving transgene expression.

Keyword: Actin depolymerizing factor Thermal asymmetric interlaced polymerase chain reaction Plectranthus amboinicus Plant promoter cis elements

Citation:

Christy SME, Aravind K, Deepika V, Selvarani ES, Arun V. Characterisation of actin depolymerising factor promoter (pTZPaADF) from Plectranthus amboinicus Lour (Spreng) using Arabidopsis thaliana (L.) Heynh as an internal control. J App Biol Biotech. 2023;11(Suppl 1):18-26. http://doi.org/10.7324/JABB.2023.144145

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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1. Wu J. Post-Transcriptional Gene Regulation: RNA Processing in Eukaryotes. United States: John Wiley and Sons; 2013. p. 280. https://doi.org/10.1002/9783527665433
2. Dynan WS, Tjian R. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. Nature 1985;316:774-8. https://doi.org/10.1038/316774a0
3. Inada N. Plant actin depolymerizing factor: Actin microfilament disassembly and more. J Plant Res 2017;130:227-38. https://doi.org/10.1007/s10265-016-0899-8
4. Kim SR, Kim Y, An G. Molecular cloning and characterization of anther-preferential cDNA encoding a putative actin-depolymerizing factor. Plant Mol Biol 1993;21:39-45. https://doi.org/10.1007/BF00039616
5. Augustine RC, Pattavina KA, Tuzel E, Vidali L, Bezanilla M. Actin interacting protein1 and actin depolymerizing factor drive rapid actindynamics in Physcomitrella patens. Plant Cell 2011;23:3696-710. https://doi.org/10.1105/tpc.111.090753
6. Huang S, Qu X, Zhang R. Plant vilins: Versatile actin regulatory proteins. J Integr Plant Biol 2015;57:40-9. https://doi.org/10.1111/jipb.12293
7. Rozycka M, Khan S, Lopez I, Greenland AJ, Hussey PJ. A Zea mays pollen cDNA encoding a putative actin-depolymerizing factor. Plant Physiol 1995;107:1011-2. https://doi.org/10.1104/pp.107.3.1011
8. Mondal HA, Louis J, Archer L, Patel M, Nalam VJ, Sarowar S, et al. Arabidopsis actin-depolymerizing factor 3 is required for controlling aphid feeding from the phloem. Plant Physiol 2018;176:879-90. https://doi.org/10.1104/pp.17.01438
9. Huang YC, Huang WL, Hong CY, Lur HS, Chang MC. Comprehensive analysis of differentially expressed rice actin depolymerizing factor gene family and heterologous overexpression of OsADF3 confers Arabidopsis thaliana drought tolerance. Rice (N Y) 2012;5:33. https://doi.org/10.1186/1939-8433-5-33
10. Tian M, Chaudhry F, Ruzicka DR, Meagher RB, Staiger CJ, Day B. Arabidopsis actin-depolymerizing factor AtADF4 mediates defense signal transduction triggered by the Pseudomonas syringae effector AvrPphB. Plant Physiol 2009;150:815-24. https://doi.org/10.1104/pp.109.137604
11. Ouellet F, Carpentier E, Cope MJ, Monroy AF, Sarhan F. Regulation of a wheat actin-depolymerizing factor during cold acclimation. Plant Physiol 2001;125:360-8. https://doi.org/10.1104/pp.125.1.360
12. Singh R, Gangwar SP, Singh D, Singh R, Pandey R, Kalra A. Medicinal plant Coleus forskohlii Briq: Disease and management. Medicinal plants. Int J Phytomed Relat Indust 2011;3:1-7. https://doi.org/10.5958/j.0975-4261.3.1.001
13. Anandhi J, Vijila C, Viswanath GS, Lokeswari TS. Screening banana plants for banana bunchy top virus with primers specific to Indian isolates. J Plant Dis Prot 2007;114:101-7. https://doi.org/10.1007/BF03356715
14. Liu YG, Whittier RF. Thermal asymmetric interlaced PCR: Automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 1995;25:674-81. https://doi.org/10.1016/0888-7543(95)80010-J
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19. Shahmuradov IA, Umarov RK, Solovyev VV. TSSPlant: A new tool for prediction of plant Pol II promoters. Nucleic Acids Res 2017;45:e65. https://doi.org/10.1093/nar/gkw1353
20. Liu YG, Mitsukawa N, Oosumi T, Whittier RF. Efficient isolation and mapping of Arabidopsis thaliana T?DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 1995;8:457-63. https://doi.org/10.1046/j.1365-313X.1995.08030457.x
21. Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol 2018;19:621-37. https://doi.org/10.1038/s41580-018-0028-8
22. Zhu Q, Dabi T, Lamb C. TATA box and initiator functions in the accurate transcription of a plant minimal promoter in vitro. Plant Cell 1995;7:1681-9. https://doi.org/10.1105/tpc.7.10.1681
23. Hajiahmadi Z, Shirzadian-Khorramabad R, Kazemzad M, Sohani MM. Enhancement of tomato resistance to Tuta absoluta using a new efficient mesoporous silica nanoparticle mediated plant transient gene expression approach. Plant Omics 2017;10:118-26. https://doi.org/10.21475/poj.10.03.17.pne411
24. Basu S, Roychoudhury A, Sengupta DN. Deciphering the role of various cis-acting regulatory elements in controlling SamDC gene expression in rice. Plant Signal Behav 2014;9:e28391. https://doi.org/10.4161/psb.28391
25. Banu SA, Huda KN, Tuteja N. Isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 using Agrobacterium-mediated transient assay. Plant Signal Behav 2014;9:e28992. https://doi.org/10.4161/psb.28992
26. Montiel G, Zarei A, Körbes AP, Memelink J. The jasmonateresponsive element from the ORCA3 promoter from Catharanthus roseus is active in Arabidopsis and is controlled by the transcription factor AtMYC2. Plant Cell Physiol 2011;52:578-87. https://doi.org/10.1093/pcp/pcr016
27. Dare AP, Schaffer RJ, Lin-Wang K. Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes. Plant Methods 2008;4:17. https://doi.org/10.1186/1746-4811-4-17
28. Tian M. Arabidopsis actin-depolymerizing factor AtADF4 mediates defence signal transduction triggered by the Pseudomonas syringae effector AvrPphB. Plant Physiol 2009;150:815-24. https://doi.org/10.1104/pp.109.137604
29. Fu Y. TaADF7, an actin-depolymerizing factor, contributes to wheat resistance against Puccinia striiformis f. sp. Tritici. Plant J 2014;78:16-30. https://doi.org/10.1111/tpj.12457
30. Mun JH. Petunia actin-depolymerizing factor is mainly accumulated in vascular tissue and its gene expression is enhanced by the first intron. Gene 2002;292:233-43. https://doi.org/10.1016/S0378-1119(02)00646-7
31. Nan Q, Qian D, Niu Y, He Y, Tong S, Niu Z, et al. Plant actin depolymerizing factors possess opposing biochemical properties arising from key amino acid changes throughout evolution. Plant Cell 2017;29:395-408. https://doi.org/10.1105/tpc.16.00690

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1. Wu J. Post-Transcriptional Gene Regulation: RNA Processing in Eukaryotes. United States: John Wiley and Sons; 2013. p. 280. https://doi.org/10.1002/9783527665433

2. Dynan WS, Tjian R. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. Nature 1985;316:774-8. https://doi.org/10.1038/316774a0

3. Inada N. Plant actin depolymerizing factor: Actin microfilament disassembly and more. J Plant Res 2017;130:227-38. https://doi.org/10.1007/s10265-016-0899-8

4. Kim SR, Kim Y, An G. Molecular cloning and characterization of anther-preferential cDNA encoding a putative actin-depolymerizing factor. Plant Mol Biol 1993;21:39-45. https://doi.org/10.1007/BF00039616

5. Augustine RC, Pattavina KA, Tuzel E, Vidali L, Bezanilla M. Actin interacting protein1 and actin depolymerizing factor drive rapid actindynamics in Physcomitrella patens. Plant Cell 2011;23:3696-710. https://doi.org/10.1105/tpc.111.090753

6. Huang S, Qu X, Zhang R. Plant vilins: Versatile actin regulatory proteins. J Integr Plant Biol 2015;57:40-9. https://doi.org/10.1111/jipb.12293

7. Rozycka M, Khan S, Lopez I, Greenland AJ, Hussey PJ. A Zea mays pollen cDNA encoding a putative actin-depolymerizing factor. Plant Physiol 1995;107:1011-2. https://doi.org/10.1104/pp.107.3.1011

8. Mondal HA, Louis J, Archer L, Patel M, Nalam VJ, Sarowar S, et al. Arabidopsis actin-depolymerizing factor 3 is required for controlling aphid feeding from the phloem. Plant Physiol 2018;176:879-90. https://doi.org/10.1104/pp.17.01438

9. Huang YC, Huang WL, Hong CY, Lur HS, Chang MC. Comprehensive analysis of differentially expressed rice actin depolymerizing factor gene family and heterologous overexpression of OsADF3 confers Arabidopsis thaliana drought tolerance. Rice (N Y) 2012;5:33. https://doi.org/10.1186/1939-8433-5-33

10. Tian M, Chaudhry F, Ruzicka DR, Meagher RB, Staiger CJ, Day B. Arabidopsis actin-depolymerizing factor AtADF4 mediates defense signal transduction triggered by the Pseudomonas syringae effector AvrPphB. Plant Physiol 2009;150:815-24. https://doi.org/10.1104/pp.109.137604

11. Ouellet F, Carpentier E, Cope MJ, Monroy AF, Sarhan F. Regulation of a wheat actin-depolymerizing factor during cold acclimation. Plant Physiol 2001;125:360-8. https://doi.org/10.1104/pp.125.1.360

12. Singh R, Gangwar SP, Singh D, Singh R, Pandey R, Kalra A. Medicinal plant Coleus forskohlii Briq: Disease and management. Medicinal plants. Int J Phytomed Relat Indust 2011;3:1-7. https://doi.org/10.5958/j.0975-4261.3.1.001

13. Anandhi J, Vijila C, Viswanath GS, Lokeswari TS. Screening banana plants for banana bunchy top virus with primers specific to Indian isolates. J Plant Dis Prot 2007;114:101-7. https://doi.org/10.1007/BF03356715

14. Liu YG, Whittier RF. Thermal asymmetric interlaced PCR: Automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 1995;25:674-81. https://doi.org/10.1016/0888-7543(95)80010-J

15. Green MR, Sambrook J. Molecular Cloning: A Laboratory Manual. 4th ed. New York: Cold Spring Harbor Laboratory Press. 2019.

16. Bolser D, Staines DM, Pritchard E, Kersey P. Ensembl plants: Integrating tools for visualizing, mining, and analysing plant genomics data. Methods Mol Biol 2016;1374:115-40. https://doi.org/10.1007/978-1-4939-3167-5_6

17. Higo K, Ugawa Y, Iwamoto M, Higo H. PLACE: A database of plant cis-acting regulatory DNA elements. Nucleic Acids Res 1998;26:358-9. https://doi.org/10.1093/nar/26.1.358

18. Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, et al. PlantCARE, a database for plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 2002;30:325-7. https://doi.org/10.1093/nar/30.1.325

19. Shahmuradov IA, Umarov RK, Solovyev VV. TSSPlant: A new tool for prediction of plant Pol II promoters. Nucleic Acids Res 2017;45:e65. https://doi.org/10.1093/nar/gkw1353

20. Liu YG, Mitsukawa N, Oosumi T, Whittier RF. Efficient isolation and mapping of Arabidopsis thaliana T?DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 1995;8:457-63. https://doi.org/10.1046/j.1365-313X.1995.08030457.x

21. Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol 2018;19:621-37. https://doi.org/10.1038/s41580-018-0028-8

22. Zhu Q, Dabi T, Lamb C. TATA box and initiator functions in the accurate transcription of a plant minimal promoter in vitro. Plant Cell 1995;7:1681-9. https://doi.org/10.1105/tpc.7.10.1681

23. Hajiahmadi Z, Shirzadian-Khorramabad R, Kazemzad M, Sohani MM. Enhancement of tomato resistance to Tuta absoluta using a new efficient mesoporous silica nanoparticle mediated plant transient gene expression approach. Plant Omics 2017;10:118-26. https://doi.org/10.21475/poj.10.03.17.pne411

24. Basu S, Roychoudhury A, Sengupta DN. Deciphering the role of various cis-acting regulatory elements in controlling SamDC gene expression in rice. Plant Signal Behav 2014;9:e28391. https://doi.org/10.4161/psb.28391

25. Banu SA, Huda KN, Tuteja N. Isolation and functional characterization of the promoter of a DEAD-box helicase Psp68 using Agrobacterium-mediated transient assay. Plant Signal Behav 2014;9:e28992. https://doi.org/10.4161/psb.28992

26. Montiel G, Zarei A, Körbes AP, Memelink J. The jasmonateresponsive element from the ORCA3 promoter from Catharanthus roseus is active in Arabidopsis and is controlled by the transcription factor AtMYC2. Plant Cell Physiol 2011;52:578-87. https://doi.org/10.1093/pcp/pcr016

27. Dare AP, Schaffer RJ, Lin-Wang K. Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes. Plant Methods 2008;4:17. https://doi.org/10.1186/1746-4811-4-17

28. Tian M. Arabidopsis actin-depolymerizing factor AtADF4 mediates defence signal transduction triggered by the Pseudomonas syringae effector AvrPphB. Plant Physiol 2009;150:815-24. https://doi.org/10.1104/pp.109.137604

29. Fu Y. TaADF7, an actin-depolymerizing factor, contributes to wheat resistance against Puccinia striiformis f. sp. Tritici. Plant J 2014;78:16-30. https://doi.org/10.1111/tpj.12457

30. Mun JH. Petunia actin-depolymerizing factor is mainly accumulated in vascular tissue and its gene expression is enhanced by the first intron. Gene 2002;292:233-43. https://doi.org/10.1016/S0378-1119(02)00646-7

31. Nan Q, Qian D, Niu Y, He Y, Tong S, Niu Z, et al. Plant actin depolymerizing factors possess opposing biochemical properties arising from key amino acid changes throughout evolution. Plant Cell 2017;29:395-408. https://doi.org/10.1105/tpc.16.00690

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