Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study

Tugba Gürkök Tan; Ceyda Nil Gökkaya; Hülya Sipahi

doi:10.17776/csj.1950348

Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study

Abstract

The Pará rubber tree (Hevea brasiliensis) is the primary commercial source of natural rubber. Latex production in this species can be significantly enhanced by ethylene stimulation, typically applied as ethephon. However, the molecular mechanisms underlying this response remain to be fully elucidated. In this study, changes in gene expression in rubber tree seedlings exposed to ethephon were investigated using bioinformatic approaches. For this purpose, microarray data (GSE174832) from the NCBI Gene Expression Omnibus were analyzed using GEO2R. Differentially expressed genes (DEGs) were identified at 24 and 48 hours post-ethephon treatment compared with controls, and DEGs shared between the two time points were selected for further analysis. Specifically, the mevalonate (MVA) and methylerythritol-4-phosphate (MEP) pathways, which provide isopentenyl diphosphate (IPP) for isoprenoid biosynthesis, together with downstream isoprenoid- and rubber-related genes, were examined. A protein-protein interaction (PPI) network was constructed to identify hub genes governing these responses. Seven genes—DXS, ISPE, HMGS, HMG1, FPS2, SQE1, and SQE3—were consistently identified as hub genes by MCC, EPC, and MCODE. Six hub genes were down-regulated at both time points, whereas ISPE was up-regulated. Functional enrichment prominently highlighted terpenoid backbone biosynthesis. FPS2 and CPT1 were down-regulated, whereas GGPPS1 was up-regulated, indicating a non-uniform transcriptional response among isoprenoid-related genes. Overall, the results do not support broad transcriptional activation of the rubber biosynthetic machinery in ethephon-treated seedling stems but identify persistent ethephon-responsive genes associated with isoprenoid metabolism. These genes represent candidates for further investigation and experimental validation in laticifer tissues.

Keywords

Ethylene, Hevea brasiliensis, Hub gene, MAP pathyway, Rubber biosynthesis

Supporting Institution

Non

Project Number

Non

Ethical Statement

Non

Thanks

Non

References

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Details

Primary Language

English

Subjects

Biological Network Analysis

Journal Section

Research Article

Authors

Tugba Gürkök Tan ^*
0000-0003-0599-5628
Türkiye

Ceyda Nil Gökkaya
0009-0007-3534-8057
Türkiye

Hülya Sipahi
0000-0002-7925-2766
Türkiye

Publication Date

October 27, 2026

Submission Date

May 13, 2026

Acceptance Date

October 17, 2026

Published in Issue

Year 2026 Volume: 47 Number: 5

DOI

https://doi.org/10.17776/csj.1950348

IZ

https://izlik.org/JA83GR78MA

APA

Gürkök Tan, T., Gökkaya, C. N., & Sipahi, H. (2026). Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study. Cumhuriyet Science Journal, 47(5), 813-820. https://doi.org/10.17776/csj.1950348

AMA

1.Gürkök Tan T, Gökkaya CN, Sipahi H. Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study. CSJ. 2026;47(5):813-820. doi:10.17776/csj.1950348

Chicago

Gürkök Tan, Tugba, Ceyda Nil Gökkaya, and Hülya Sipahi. 2026. “Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea Brasiliensis Seedlings: A Bioinformatic Study”. Cumhuriyet Science Journal 47 (5): 813-20. https://doi.org/10.17776/csj.1950348.

EndNote

Gürkök Tan T, Gökkaya CN, Sipahi H (October 1, 2026) Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study. Cumhuriyet Science Journal 47 5 813–820.

IEEE

[1]T. Gürkök Tan, C. N. Gökkaya, and H. Sipahi, “Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study”, CSJ, vol. 47, no. 5, pp. 813–820, Oct. 2026, doi: 10.17776/csj.1950348.

ISNAD

Gürkök Tan, Tugba - Gökkaya, Ceyda Nil - Sipahi, Hülya. “Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea Brasiliensis Seedlings: A Bioinformatic Study”. Cumhuriyet Science Journal 47/5 (October 1, 2026): 813-820. https://doi.org/10.17776/csj.1950348.

JAMA

1.Gürkök Tan T, Gökkaya CN, Sipahi H. Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study. CSJ. 2026;47:813–820.

MLA

Gürkök Tan, Tugba, et al. “Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea Brasiliensis Seedlings: A Bioinformatic Study”. Cumhuriyet Science Journal, vol. 47, no. 5, Oct. 2026, pp. 813-20, doi:10.17776/csj.1950348.

Vancouver

1.Tugba Gürkök Tan, Ceyda Nil Gökkaya, Hülya Sipahi. Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study. CSJ. 2026 Oct. 1;47(5):813-20. doi:10.17776/csj.1950348

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Identification of Key Hub Genes and Their Role in Regulating IPP Biosynthesis Pathways in Ethylene-Stimulated Hevea brasiliensis Seedlings: A Bioinformatic Study

Abstract

Keywords

Supporting Institution

Project Number

Ethical Statement

Thanks

References

Details

Primary Language

Subjects

Journal Section

Authors

Publication Date

Submission Date

Acceptance Date

Published in Issue

DOI

IZ

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