Stout Kafur Ağacında LEA Genlerinin Biyoinformatik Analizi (Cinnamomum micranthum f. Kanehirae)

Yıl 2024, , 86 - 97, 31.08.2024

Tevfik Hasan Can , Tamer Kuşaksız

https://doi.org/10.55507/gopzfd.1517870

Öz

LEA proteinleri bitkilerin abiyotik streslere karşı tepkilerinde önemli bir role sahiptir. Lauraceae ailesine ait tıbbi ve aromatik bir bitki olan Cinnamomum micranthum f. Kanehirae veya Stout Kafur ağacının genom dizisi yakın zamanda tamamlanmıştır. Stout Kafur genomunda çalışmalar olmasına rağmen LEA genleri ile alakalı herhangi bir çalışma bulunmamaktadır. Bu nedenle bu çalışmada biyoinformatik araçlar kullanılarak Stout Kafur genomunda yer alan LEA genlerinin genom çapında analizinin yapılması amaçlanmıştır.
Stout Kafur genomunda 57 LEA geni (CmiLEA) tanımlandı. CmiLEA filogenetik analize göre 8 ayrı kümeye ayrılmıştır. CmiLEA'nın subselüler lokalizasyonları incelendiğinde daha çok sitoplazmada lokalize oldukları ve sadece bir miRNA hedefleyen toplam 13 gen tanımlanmıştır. CmiLEA’ da toplam 23 genin yalnızca ekzon bölgelerine sahip olduğu ve intronsuz olduğu tespit edilmiştir. Toplamda 35 korunmuş motif belirlenirken, CmiLEA-42'de yalnızca bir korunmuş motif bulunmuştur. 3B yapı sonuçlarına uygun olarak LEA_2 alt ailesinden CmiLEA-21, CmiLEA-31, CmiLEA-44, CmiLEA-45 ve CmiLEA-57 %90'ın üzerinde doğruluk göstermiştir.
Bu çalışma, Cinnamomum micranthum f. kanehirae bitkisinde LEA genleri ile ilgili yapılmış ilk biyoinformatik çalışma olup, Cinnamomum cinsinde gelecekte ileri fonksiyonel analizler için bir temel oluşturabileceği düşünülmektedir.

Anahtar Kelimeler

Biyoinformatik, LEA genleri, LEA proteinleri, miRNA, Stout Kafur Ağacı

Bioinformatic Analysis of LEA Genes in Stout Camphor Tree (Cinnamomum micranthum f. Kanehirae)

Öz

LEA proteins have an important role in the response of plants to abiotic stresses. Cinnamomum micranthum f. kanehirae, a medicinal and aromatic plant belonging to the Lauraceae family. The genome sequence of the Kanehirae or Stout Camphor tree was recently completed. Although there are studies on its genome, there are no studies on LEA genes.
57 LEA genes (CmiLEA) were identified in the Stout Camphor genome. CmiLEA was divided into 8 distinct clusters based on phylogenetic analysis. When the subcellular localizations of CmiLEA were examined, they were found to be localized mostly in the cytoplasm. A total of 13 genes targeting only one miRNA were identified. In CmiLEA, a total of 23 genes were found to have only exon regions and no introns. In total, 35 conserved motifs were identified, while there was only one conserved motif in CmiLEA-42. Consistent with the 3D structure results, CmiLEA-21, CmiLEA-31, CmiLEA-44, CmiLEA-45, and CmiLEA-57 from the LEA-2 subfamily showed over 90% accuracy.
The present study was the first in-silico analysis of LEA genes in Cinnamomum micranthum f. Kanehirae. It is thought that it may form a base for advanced functional analysis in Cinnamomum in future.

Anahtar Kelimeler

Bioinformatics, LEA genes, LEA proteins, miRNA, Stout Camphor Tree

Kaynakça

• Aziz, M. A., Sabeem, M., Kutty, M. S., Rahman, S., Alneyadi, M. K., Alkaabi, A. B., & Masmoudi, K. (2023). Enzyme stabilization and thermotolerance function of the intrinsically disordered LEA2 proteins from date palm. Scientific reports, 13(1), 11878.
• Bailey, T. L., Johnson, J., Grant, C. E., & Noble, W. S. (2015). The MEME suite. Nucleic acids research, 43(W1), W39-W49.
• Bies-Etheve, N., Gaubier-Comella, P., Debures, A., Lasserre, E., Jobet, E., Raynal, M., Cooke, & Delseny, M. (2008). Inventory, evolution and expression profiling diversity of the LEA (late embryogenesis abundant) protein gene family in Arabidopsis thaliana. Plant molecular biology, 67, 107-124.
• Breakfield, N. W., Corcoran, D. L., Petricka, J. J., Shen, J., Sae-Seaw, J., Rubio-Somoza, I., R., Weigel, D., Ohler, U.& Benfey, P. N. (2012). High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome research, 22(1), 163-176.
• Celik Altunoglu, Y., Baloglu, M. C., Baloglu, P., Yer, E. N., & Kara, S. (2017). Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes. Physiology and Molecular Biology of Plants, 23, 5-21.
• Chang, C. J., Lu, C. C., Lin, C. S., Martel, J., Ko, Y. F., Ojcius, D. M. & Young, J. D. (2018). Antrodia cinnamomea reduces obesity and modulates the gut microbiota in high-fat diet-fed mice. International journal of obesity, 42(2), 231-243.
• Chen, L., Xin, J., Song, H., Xu, F., Yang, H., Sun, H., & Yang, M. (2023). Genome-wide study and functional characterization elucidates the potential association of late embryogenesis abundant (LEA) genes with lotus seed development. International Journal of Biological Macromolecules, 226, 1-13.
• Cheng, Z., Zhang, X., Yao, W., Zhao, K., Liu, L., Fan, G., ... & Jiang, T. (2021). Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar. BMC Plant Biology, 21, 1-17.
• Chung, K. F., & Hsieh, C. L. (2023). Synopsis of Camphora (Cinnamomeae, Lauraceae) of Taiwan, with two new combinations and one new synonym. Taiwania, 68(3).
• Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18), 3674-3676.
• Dai, X., Zhuang, Z., & Zhao, P. X. (2018). psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic acids research, 46(W1), W49-W54.
• Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S. E., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server (pp. 571-607). Humana press.
• Geng, W., Wang, Y., Zhang, J., Liu, Z., Chen, X., Qin, L., Yang, L. & Tang, H. (2022). Genome-wide identification and expression analyses of late embryogenesis abundant (LEA) gene family in tobacco (Nicotiana tabacum L.) reveal their function in abiotic stress responses. Gene, 836, 146665.
• Hong-Bo, S., Zong-Suo, L., & Ming-An, S. (2005). LEA proteins in higher plants: structure, function, gene expression and regulation. Colloids and surfaces B: Biointerfaces, 45(3-4), 131-135.
• Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8), 1296-1297.
• Huang, R., Xiao, D., Wang, X., Zhan, J., Wang, A., & He, L. (2022). Genome-wide identification, evolutionary and expression analyses of LEA gene family in peanut (Arachis hypogaea L.). BMC Plant Biology, 22(1), 155.
• Hundertmark, M., & Hincha, D. K. (2008). LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC genomics, 9, 1-22.
• Jiang, R., Chen, X., Liao, X., Peng, D., Han, X., Zhu, C., ... & Li, C. (2022). A chromosome-level genome of the camphor tree and the underlying genetic and climatic factors for its top-geoherbalism. Frontiers in Plant Science, 13, 827890.
• Jones-Rhoades, M. W., & Bartel, D. P. (2004). Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular cell, 14(6), 787-799.
• Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature protocols, 10(6), 845-858.
• Kozomara, A., Birgaoanu, M., & Griffiths-Jones, S. (2019). miRBase: from microRNA sequences to function. Nucleic acids research, 47(D1), D155-D162.
• Li, D., Lin, H. Y., Wang, X., Bi, B., Gao, Y., Shao, L. & Zhang, L. (2023). Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes. BMC biology, 21(1), 192.
• Li, Y., Qi, S., Chen, S., Li, H., Zhang, T., Bao, F. & Zhao, J. (2023). Genome-wide identification and expression analysis of late embryogenesis abundant (LEA) genes reveal their potential roles in somatic embryogenesis in hybrid sweetgum (Liquidambar styraciflua× Liquidambar formosana). Forestry Research, 3(1).
• Li, Z., Chi, H., Liu, C., Zhang, T., Han, L., Li, L., Pei, X. & Long, Y. (2021). Genome-wide identification and functional characterization of LEA genes during seed development process in linseed flax (Linum usitatissimum L.). BMC Plant Biology, 21, 1-13.
• Liang, G., Ai, Q., & Yu, D. (2015). Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis. Scientific reports, 5(1), 11813.
• Liang, G., He, H., & Yu, D. (2012). Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana. PloS one, 7(11), e48951.
• Lin, R., Zou, T., Mei, Q., Wang, Z., Zhang, M., & Jian, S. (2021). Genome-wide analysis of the late embryogenesis abundant (LEA) and abscisic acid-, stress-, and ripening-induced (ASR) gene superfamily from Canavalia rosea and their roles in salinity/alkaline and drought tolerance. International Journal of Molecular Sciences, 22(9), 4554.
• Lin, R., Zou, T., Mei, Q., Wang, Z., Zhang, M., & Jian, S. (2021). Genome-wide analysis of the late embryogenesis abundant (LEA) and abscisic acid-, stress-, and ripening-induced (ASR) gene superfamily from Canavalia rosea and their roles in salinity/alkaline and drought tolerance. International Journal of Molecular Sciences, 22(9), 4554.
• NCBI. (2024). https://www.ncbi.nlm.nih.gov/.
• Qiagen, 2022. CLC Genomic Workbench 21. https://digitalinsights.qiagen.com/.
• Rakhmetullina, A., Zielenkiewicz, P., Pyrkova, A., Uteulin, K., & Ivashchenko, A. (2021). Prediction of characteristics of interactions of miRNA with mRNA of GRAS, ERF, C2H2 genes of A. thaliana, O. sativa and Z. mays. Current Plant Biology, 28, 100224.
• Shao, C., Wu, Q., Qiu, J., Jin, S., Zhang, B., Qian, J., Chen, M. & Meng, Y. (2013). Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis. Gene, 527(2), 477-483.
• Shen, T., Qi, H., Luan, X., Xu, W., Yu, F., Zhong, Y., & Xu, M. (2022). The chromosome‐level genome sequence of the camphor tree provides insights into Lauraceae evolution and terpene biosynthesis. Plant Biotechnology Journal, 20(2), 244.
• Sun, W. H., Xiang, S., Zhang, Q. G., Xiao, L., Zhang, D. Y., Zhang, P. L. & Zou, S. Q. (2022). The camphor tree genome enhances the understanding of magnoliid evolution.
• Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: molecular evolutionary genetics analysis version 11. Molecular biology and evolution, 38 (7), 3022-3027.
• Thatcher, S. R., Burd, S., Wright, C., Lers, A., & Green, P. J. (2015). Differential expression of miRNAs and their target genes in senescing leaves and siliques: insights from deep sequencing of small RNAs and cleaved target RNAs. Plant, cell & environment, 38(1), 188-200.
• Vidal, E. A., Moyano, T. C., Krouk, G., Katari, M. S., Tanurdzic, M., McCombie, W. R. & Gutiérrez, R. A. (2013). Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC genomics, 14, 1-15.
• Wang, X. D., Xu, C. Y., Zheng, Y. J., Wu, Y. F., Zhang, Y. T., Zhang, T. & Jiang, X. M. (2022). Chromosome-level genome assembly and resequencing of camphor tree (Cinnamomum camphora) provides insight into phylogeny and diversification of terpenoid and triglyceride biosynthesis of Cinnamomum. Horticulture Research, 9, uhac216.