Have a personal or library account? Click to login
A note on the nomenclatural representation of plant transcription factors, and deviations thereof Cover

A note on the nomenclatural representation of plant transcription factors, and deviations thereof

Open Access
|Oct 2024

References

  1. Ailizati, A., Nagahage, I. S. P., Miyagi, A., Ishikawa, T., Kawai-Yamada, M., Demura, T., & Yamaguchi, M. (2022). VND-INTERACTING2 effectively inhibits transcriptional activities of VASCULAR-RELATED NAC-DOMAIN7 through a conserved sequence. Plant Biotechnology, 39(2), 147–153. https://doi.org/10.5511/plantbiotechnology.22.0122a
  2. Allan, A. C. (2019). Domestication: Colour and flavour joined by a shared transcription factor. Current Biology, 29(2), R57–R59. https://doi.org/10.1016/j.cub.2018.12.005
  3. Alshareef, N. O., Otterbach, S. L., Allu, A. D., Woo, Y. H., de Werk, T., Kamranfar, I., Mueller-Roeber, B., Tester, M., Balazadeh, S., & Schmöckel, S. M. (2022). NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis. Scientific Reports, 12(1), 11264. https://doi.org/10.1038/s41598-022-14429-x
  4. Barco, B., & Clay, N. K. (2020). Hierarchical and dynamic regulation of defense-responsive specialized metabolism by WRKY and MYB transcription factors. Frontiers in Plant Science, 10, 1775. https://doi.org/10.3389/fpls.2019.01775
  5. Blanc-Mathieu, R., Dumas, R., Turchi, L., Lucas, J., & Parcy, F. (2024). Plant-TFClass: A structural classification for plant transcription factors. Trends in Plant Science, 29(1), 40–51. https://doi.org/10.1016/j.tplants.2023.06.023
  6. Brian, L., Warren, B., McAtee, P., Rodrigues, J., Nieuwenhuizen, N., Pasha, A., David, K. M., Richardson, A., Provart, N. J., Allan, A. C., Varkonyi-Gasic, E., & Schaffer, R. J. (2021). A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors. BMC Plant Biology, 21(1), 121. https://doi.org/10.1186/s12870-021-02894-x
  7. Butelli, E., Licciardello, C., Ramadugu, C., Durand-Hulak, M., Celant, A., Reforgiato Recupero, G., Froelicher, Y., & Martin, C. (2019). Noemi controls production of flavonoid pigments and fruit acidity and illustrates the domestication routes of modern citrus varieties. Current Biology, 29(1), 158–164.e2. https://doi.org/10.1016/j.cub.2018.11.040
  8. Chow, C. N., Yang, C. W., Wu, N. Y., Wang, H. T., Tseng, K. C., Chiu, Y. H., Lee, T. Y., & Chang, W. C. (2024). PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters. Nucleic Acids Research, 52(D1), D1569–D1578. https://doi.org/10.1093/nar/gkad945
  9. Dang, X., Zhang, B., Li, C., & Nagawa, S. (2022). FvNST1b NAC protein induces secondary cell wall formation in strawberry. International Journal of Molecular Sciences, 23(21), 13212. https://doi.org/10.3390/ijms232113212
  10. Gong, X., Zhao, L-Y., Song, X-F., Lin, Z-K., Gu, B-J., Yan, J-X., Zhang, S-L., Tao, S-T., & Huang, X-S. (2019). Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri). BMC Plant Biology, 19(1), 161. https://doi.org/10.1186/s12870-019-1760-8
  11. Gray, J., Bevan, M., Brutnell, T., Buell, C. R., Cone, K., Hake, S., Jackson, D., Kellogg, E., Lawrence, C., McCouch, S., Mockler, T., Moose, S., Paterson, A., Peterson, T., Rokshar, D., Souza, G. M., Springer, N., Stein, N., Timmermans, M., Wang, G. L., & Grotewold, E. (2009). A recommendation for naming transcription factor proteins in the grasses. Plant Physiology, 149(1), 4–6. https://doi.org/10.1104/pp.108.128504
  12. Hartmann, A., Berkowitz, O., Whelan, J., & Narsai, R. (2022). Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment. BMC Plant Biology, 22(1), 62. https://doi.org/10.1186/s12870-021-03406-7
  13. Hetz, C., Zhang, K. & Kaufman, R.J. (2020). Mechanisms, regulation and functions of the unfolded protein response. Nature Reviews Molecular Cell Biology, 21, 421–438. https://doi.org/10.1038/s41580-020-0250-z
  14. Hrmova, M., & Hussain, S.S. (2021). Plant transcription factors involved in drought and associated stresses. International Journal of Molecular Sciences, 22(11), 5662. https://doi.org/10.3390/ijms22115662
  15. Hu, X-L., Xie, F-F., Liang, W-W., Liang, Y-H., Zhang, Z-K., Zhao, J-T., Hu, G-B., & Qin, Y-H. (2022). HuNAC20 and HuNAC25, two novel NAC genes from pitaya, confer cold tolerance in transgenic Arabidopsis. International Journal of Molecular Sciences, 23(4), 2189. https://doi.org/10.3390/ijms23042189
  16. Jan, S. U., Jamil, M., Bhatti, M. F., & Gul, A. (2019). Hallmark attributes of plant transcription factors and potentials of WRKY, MYB and NAC in abiotic stresses. In: Hasanuzzaman, M., Nahar, K., Fujita, M., Oku, H., Tofazzal, M. I. (eds.) Approaches for Enhancing Abiotic Stress Tolerance in Plants, CRC Press, Boca Raton, pp. 441–458.
  17. Karppinen, K., Lafferty, D. J., Albert, N. W., Mikkola, N., McGhie, T., Allan, A. C., Afzal, B. M., Häggman, H., Espley, R. V., & Jaakola, L. (2021). MYBA and MYBPA transcription factors co-regulate anthocyanin biosynthesis in blue-coloured berries. New Phytologist, 232(3), 1350–1367. https://doi.org/10.1111/nph.17669
  18. Lai, X., Chahtane, H., Martin-Arevalillo, R., Zubieta, C., & Parcy, F. (2020). Contrasted evolutionary trajectories of plant transcription factors. Current Opinion in Plant Biology, 54, 101–107. https://doi.org/10.1016/j.pbi.2020.03.002
  19. Li, F., Shan, Y., Wang, H., Jiang, G., Ding, X., Liang, H., Wang, C., Kong, X., Xie, L., & Jiang, Y. (2023). A NAC transcriptional factor BrNAC029 is involved in cytokinin-delayed leaf senescence in postharvest Chinese flowering cabbage. Food Chemistry, 404(Pt B), 134657. https://doi.org/10.1016/j.foodchem.2022.134657
  20. Li, P-T., Chai, Z., Lin, P-P., Huang, C-H., Huang, G-Q., Xu, L-N., Deng, Z-H., Zhang, M-Q., Zhang, Y., & Zhao, X-W. (2020). Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.). BMC Genomics, 21(1), 685. https://doi.org/10.1186/s12864-020-07076-x
  21. Li, Q., Zhou, L-Y., Li, Y-H., Zhang, D-P., & Gao, Y. (2021). Plant NIGT1/HRS1/HHO transcription factors: Key regulators with multiple roles in plant growth, development, and stress responses. International Journal of Molecular Sciences, 22(16), 8685. https://doi.org/10.3390/ijms22168685
  22. Li, X., Wang, Q., Guo, C., Sun, J., Li, Z., Wang, Y., Yang, A., Pu, W., Guo, Y., Gao, J., & Wen, L. (2022). NtNAC053, a novel NAC transcription factor, confers drought and salt tolerances in tobacco. Frontiers in Plant Science, 13, 817106. https://doi.org/10.3389/fpls.2022.817106
  23. Liu, X., Zong, X., Wu, X., Liu, H., Han, J., Yao, Z., Ren, Y., Ma, L., Wang, B., & Zhang, H. (2022). Ectopic expression of NAC transcription factor HaNAC3 from Haloxylon ammodendron increased abiotic stress resistance in tobacco. Planta, 256(6), 105. https://doi.org/10.1007/s00425-022-04021-y
  24. Ma, W-H., Kang, X., Liu, P., She, K-X., Zhang, Y-Y., Lin, X-R., Li, B., & Chen, Z-Z. (2022). The NAC-like transcription factor CsNAC7 positively regulates the caffeine biosynthesis-related gene yhNMT1 in Camellia sinensis. Horticulture Research, 9, uhab046. https://doi.org/10.1093/hr/uhab046
  25. Mao, H., Li, S-M., Chen, B., Jian, C., Mei, F-M., Zhang, Y-F., Li, F-F., Chen, N., Li, T., Du, L-Y., Ding, L., Wang, Z-X., Cheng, X-X., Wang, X-J., & Kang, Z-S. (2022). Variation in cis-regulation of a NAC transcription factor contributes to drought tolerance in wheat. Molecular Plant, 15(2), 276–292. https://doi.org/10.1016/j.molp.2021.11.007
  26. Meng, L., Yang, H., Xiang, L., Wang, Y., & Chan, Z. (2022). NAC transcription factor TgNAP promotes tulip petal senescence. Plant Physiology, 190(3), 1960–1977. https://doi.org/10.1093/plphys/kiac351
  27. Mijiti, M., Wang, Y., Wang, L., & Habuding, X. (2022). Tamarix hispida NAC transcription factor ThNAC4 [sic] confers salt and drought stress tolerance to transgenic Tamarix and Arabidopsis. Plants, 11(19), 2647. https://doi.org/10.3390/plants11192647
  28. Ng, D.W.-K., Abeysinghe, J.K., & Kamali, M. (2018). Regulating the regulators: The control of transcription factors in plant defense signaling. International Journal of Molecular Sciences, 19(12), 3737. https://doi.org/10.3390/ijms19123737
  29. Niu, X-L., & Fu, D-Q. (2022). The Roles of BLH transcription factors in plant development and environmental response. International Journal of Molecular Sciences, 23(7), 3731. https://doi.org/10.3390/ijms23073731
  30. Peng, H., Phung, J., Stowe, E. C., Dhingra, A., & Neff, M. M. (2022). The NAC transcription factor ATAF2 promotes ethylene biosynthesis and response in Arabidopsis thaliana seedlings. FEBS Letters, 596(12), 1586–1599. https://doi.org/10.1002/1873-3468.14317
  31. PlantRegMap (2024). PlantRegMap/PlantTFDB v5.0. Plant Transcription Factor Database. http://planttfdb.gaolab.org/help_famschema.php (last accessed: 25 July 2024)
  32. PubMed (2024). Plants NAC. https://pubmed.ncbi.nlm.nih.gov/?term=plants+NAC (last access: 25 July 2024)
  33. Romani, F., & Moreno, J. E. (2021). Molecular mechanisms involved in functional macroevolution of plant transcription factors. New Phytologist, 230(4), 1345–1353. https://doi.org/10.1111/nph.17161
  34. Roy, D., & Sadanandom, A. (2021). SUMO mediated regulation of transcription factors as a mechanism for transducing environmental cues into cellular signaling in plants. Cellular and Molecular Life Sciences, 78(6), 2641–2664. https://doi.org/10.1007/s00018-020-03723-4
  35. Salaün, C., Lepiniec, L., & Dubreucq, B. (2021). Genetic and molecular control of somatic embryogenesis. Plants, 10(7), 1467. https://doi.org/10.3390/plants10071467
  36. Tao, Y., Wan, J. X., Liu, Y. S., Yang, X. Z., Shen, R. F., & Zhu, X. F. (2022). The NAC transcription factor ANAC017 regulates aluminum tolerance by regulating the cell wall-modifying genes. Plant Physiology, 189(4), 2517–2534. https://doi.org/10.1093/plphys/kiac197
  37. Teixeira da Silva, J. A. (2016a). In defense of the use of italic for Latin binomial plant names. Polish Botanical Journal, 61(1), 1–6. https://doi.org/10.1515/pbj-2016-0014
  38. Teixeira da Silva, J. A. (2016b). An error is an error… is an erratum. The ethics of not correcting errors in the science literature. Publishing Research Quarterly, 32(3), 220–226. https://doi.org/10.1007/s12109-016-9469-0
  39. Teixeira da Silva, J. A. (2020). Chinese names in the biomedical literature: Suggested bibliometric standardization. Publishing Research Quarterly, 36(2), 254–257. https://doi.org/10.1007/s12109-020-09725-1
  40. Teixeira da Silva, J. A. (2023). Is the validity, credibility and reliability of literature indexed in PubMed at risk? Medical Journal Armed Forces India, 79(5), 601–602. https://doi.org/10.1016/j.mjafi.2021.03.009
  41. Teixeira da Silva, J. A. (2022). A synthesis of the formats for correcting erroneous and fraudulent academic literature, and associated challenges. Journal for General Philosophy of Science, 53(4), 583–599. https://doi.org/10.1007/s10838-022-09607-4
  42. Teixeira da Silva, J. A., Bornemann-Cimenti, H., Daly, T., & Türp, J. C. (2024). Beyond disclaimers: The need for a curation-based model of PubMed. Current Medical Research & Opinion, 40(6), 1039–1045. https://doi.org/10.1080/03007995.2024.2350612
  43. Teixeira da Silva, J. A., & Nazarovets, S. (2022). Publication history: A double DOI-based method to store and/or monitor information about published and corrected academic literature. Journal of Scholarly Publishing, 53(2), 85–108. https://doi.org/10.3138/jsp.53.2.2017-0017
  44. Tian, F., Yang, D-C., Meng, Y-Q., Jin, J-P., & Gao, G. (2020). PlantRegMap: Charting functional regulatory maps in plants. Nucleic Acids Research, 48(D1), D1104–D1113. https://doi.org/10.1093/nar/gkz1020
  45. Valoroso, M. C., Lucibelli, F., & Aceto, S. (2022). Orchid NAC transcription factors: A focused analysis of CUPULIFORMIS genes. Genes, 13(12), 2293. https://doi.org/10.3390/genes13122293
  46. Vargas-Hernández, B. Y., Núñez-Muñoz, L., Calderón-Pérez, B., Xoconostle-Cázares, B., & Ruiz-Medrano, R. (2022). The NAC transcription factor ANAC087 [sic] induces aerial rosette development and leaf senescence in Arabidopsis. Frontiers in Plant Science, 13, 818107. https://doi.org/10.3389/fpls.2022.818107
  47. Wang, M., Ren, L. T., Wei, X. Y., Ling, Y. M., Gu, H. T., Wang, S. S., Ma, X. F., & Kong, G. C. (2022). NAC transcription factor TwNAC01 [sic] positively regulates drought stress responses in Arabidopsis and Triticale. Frontiers in Plant Science, 13, 877016. https://doi.org/10.3389/fpls.2022.877016
  48. Wang, P-T., Xu, X., Tang, Z., Zhang, W-W., Huang, X-Y., & Zhao, F-J. (2018). OsWRKY28 regulates phosphate and arsenate accumulation, root system architecture and fertility in rice. Frontiers in Plant Science, 9, 1330. https://doi.org/10.3389/fpls.2018.01330
  49. Wang, X-P., Niu, Y-L., & Zheng, Y. (2021). Multiple functions of MYB transcription factors in abiotic stress responses. International Journal of Molecular Sciences, 22(11), 6125. https://doi.org/10.3390/ijms22116125
  50. Wang, Y., Cui, Y., Liu, B., Wang, Y., Sun, S., Wang, J., Tan, M., Yan, H., & Zhang, Y. (2022). Lilium pumilum stress-responsive NAC transcription factor LpNAC17 [sic] enhances salt stress tolerance in tobacco. Frontiers in Plant Science, 13, 993841. https://doi.org/10.3389/fpls.2022.993841
  51. Wani, S. H., Anand, S., Singh, B., Bohra, A., & Joshi, R. (2021). WRKY transcription factors and plant defense responses: Latest discoveries and future prospects. Plant Cell Reports, 40(7), 1071–1085. https://doi.org/10.1007/s00299-021-02691-8
  52. Xiao, R-X., Zhang, C., Guo, X-R., Li, H., & Lu, H. (2021). MYB transcription factors and its regulation in secondary cell wall formation and lignin biosynthesis during xylem development. International Journal of Molecular Sciences, 22(7), 3560. https://doi.org/10.3390/ijms22073560
  53. Xu, P-P., Ma, W., Hu, J-B., & Cai, W-M. (2022). The nitrateinducible NAC transcription factor NAC056 controls nitrate assimilation and promotes lateral root growth in Arabidopsis thaliana. PLoS Genetics, 18(3), e1010090. https://doi.org/10.1371/journal.pgen.1010090
  54. Yang, C., Huang, Y., Lv, P., Antwi-Boasiako, A., Begum, N., Zhao, T., & Zhao, J. (2022). NAC transcription factor GmNAC12 [sic] improved drought stress tolerance in soybean. International Journal of Molecular Sciences, 23(19), 12029. https://doi.org/10.3390/ijms231912029
  55. Yang, Y-H., Liu, X., Zhang, W-B., Qian, Q., Zhou, L-M., Liu, S., Li, Y-G., & Hou, X-L. (2021). Stress response proteins NRP1 and NRP2 are pro-survival factors that inhibit cell death during ER stress. Plant Physiology, 187(3), 1414–1427. https://doi.org/10.1093/plphys/kiab335
  56. Yoon, Y-D., Seo, D-H., Shin, H-Y., Kim, H-J., Kim, C-M., & Jang, G-P. (2020). The role of stress-responsive transcription factors in modulating abiotic stress tolerance in plants. Agronomy, 10(6), 788. https://doi.org/10.3390/agronomy10060788
  57. Yu, C-Y., Cho, Y., Sharma, O., & Kanehara, K. (2022). What’s unique? The unfolded protein response in plants. Journal of Experimental Botany, 73(5), 1268–1276. https://doi.org/10.1093/jxb/erab513
  58. Yu, G., Xie, Z., Lei, S., Li, H., Xu, B., & Huang, B. (2022). The NAC factor LpNAL delays leaf senescence by repressing two chlorophyll catabolic genes in perennial ryegrass. Plant Physiology, 189(2), 595–610. https://doi.org/10.1093/plphys/kiac070
  59. Zhang, J-C., Mei, H., Lu, H-J., Chen, R., Hu, Y., & Zhang, T-Z. (2022). Transcriptome time-course analysis in the whole period of cotton fiber development. Frontiers in Plant Science, 13, 864529. https://doi.org/10.3389/fpls.2022.864529
  60. Zhang, X., Li, L., Lang, Z., Li, D., He, Y., Zhao, Y., Tao, H., Wei, J., Li, Q., & Hong, G. (2022). Genome-wide characterization of NAC transcription factors in Camellia sinensis and the involvement of CsNAC28 in drought tolerance. Frontiers in Plant Science, 13, 1065261. https://doi.org/10.3389/fpls.2022.1065261
Language: English
Page range: 168 - 175
Published on: Oct 17, 2024
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2024 Jaime A. Teixeira da Silva, published by European Biotechnology Thematic Network Association
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.