The in silico study of the COBRA gene family in sugarcane related to potential biomass content


  • Riza Arief PUTRANTO Indonesian Research Institute for Biotechnology and Bioindustry
  • Galuh Wening PERMATASARI Indonesian Research Institute for Biotechnology and Bioindustry
  • Rizka Tamania SAPTARI Indonesian Research Institute for Biotechnology and Bioindustry



cellulose, comparative genomic, Saccharum sp.



Sugarcane (Saccharum sp.) is potential as a biofuel and biomaterial source for its high cellulose content. Cellulose is the main constituent of the plant cell wall, as a linear chain arranged in a polysaccharide bundle, called cellulose microfibril. A gene named COBRA has been revealed to play role in the orientation of microfibril and cellulose crystallization. The COBRA gene in the Saccharum spp is under-explored. Therefore, the in silico study was conducted to explore the COBRA gene in Saccharum sp. By comparative genomics methods, the COBRA genes from Arabidopsis sp. (AtCOBLs) were compared to the Saccharum sp. (SoCOBLs). The conserved domain was then identified and the cluster system was constructed under a phylogenetic tree. Furthermore, each SoCOBLs protein was modelled to analyze its structure. According to the analysis, eleven of Saccharum sp. genomic scaffolds were successfully identified. Moreover, conserved domain identification resulted in nine SoCOBLs proteins. The phylogenetic tree showed two main clusters: I and II, differentiating those COBLs families based on the protein sequence, domain motif and amino acid properties. It leads to the variation of SoCOBLs protein structure as the results of the amino acid properties. Overall, the COBRA gene has been identified genomically in Saccharum sp. Yet, the function and tissue-specific expression are still unclear. It was predicted to act as the regulator of microfibril orientation and the cellulose synthesis process. Hence, further analyses by in vitro and in vivo are indispensable.

[Keywords: cellulose, comparative genomic, Saccharum sp.]


Tanaman tebu (Saccharum sp.) berpotensi sebagai sumber bahan bakar nabati dan biomaterial karena kandungan selulosanya yang tinggi. Selulosa merupakan komponen utama penyusun dinding sel tanaman, sebagai rantai lurus yang tersusun dalam gugusan polisakarida, yang disebut mikrofibril selulosa. Sebuah gen bernama COBRA telah diketahui berperan dalam menentukan arah mikrofibril dan kristalisasi selulosa. Gen COBRA pada spesies Saccharum spp. belum banyak dipelajari. Oleh karena itu, kajian in silico dilakukan untuk mempelajari gen COBRA pada Saccharum sp. Melalui metode perbandingan genomika, gen COBRA dari Arabidopsis sp. (AtCOBLs) dibandingkan dengan gen COBRA dari Saccharum sp. (SoCOBLs). Domain conserve pada gen kemudian diidentifikasi dan sistem klaster disusun dalam sebuah pohon filogeni. Setelah itu, dibuat model untuk menganalisis struktur dari protein SoCOBL. Dari hasil analisis, sebelas perancah genom Saccharum sp. berhasil diidentifikasi. Kemudian, identifikasi daerah lestari menghasilkan sembilan protein SoCOBL. Pohon filogeni menggambarkan dua klaster utama: I dan II, yang membedakan famili SoCOBLs tersebut berdasarkan sekuens protein, motif domain, dan karakteristik asam amino. Karakteristik asam amino menyebabkan variasi pada struktur protein-protein SoCOBL. Secara umum, gen COBRA telah teridentifikasi pada Saccharum sp., meskipun fungsi dan ekspresi spesifiknya pada jaringan masih belum diketahui. Diperkirakan gen tersebut berperan sebagai pengatur arah mikrofibril dan proses sintesis selulosa. Oleh karena itu, perlu adanya analisis lebih lanjut pada level in vitro dan in vivo.

[Kata kunci: selulosa, genomika komparatif, Saccharum sp.]



Download data is not yet available.


Borner GHH, KS Lilley, TJ Stevens & P Dupree (2003). Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol 132(2), 568–577.

Brady SM, S Song, KS Dhugga, JA Rafalski & PN Benfey (2007). Combining expression and comparative evolutionary analysis the COBRA gene family. Plant Physiol 143(1), 172.

Brigham C (2018). Biopolymers: Biodegradable alternatives to traditional plastics. In: Green chemistry: An inclusive approach. Elsevier Inc. p. 753–770.

Cao Y, X Tang, J Giovannoni, F Xiao & Y Liu (2012). Functional characterization of a tomato COBRA-like gene functioning in fruit development and ripening. BMC Plant Biol 12(1), 211.

Dai X, C You, G Chen, X Li, Q Zhang & C Wu (2011). OsBC1L4 encodes a COBRA-like protein that affects cellulose synthesis in rice. Plant Molec Biol 75(4–5), 333–345.

Endler A, C Sánchez-Rodríguez & S Persson (2010). Cellulose squeezes through. Nat Chem Biol 6(12), 883–884.

Fan M, A Zhang, G Ye, H Zhang & J Xie (2018). Integrating sugarcane molasses into sequential cellulosic biofuel production based on SSF process of high solid loading. Biotechnol Biofuels 11, 329.

Geng H, Z Yuan, Q Fan, X Dai, Y Zhao, Z Wang & M Qin (2014). Characterisation of cellulose films regenerated from acetone/water coagulants. Carbohydr Polym 102, 438 – 444.

Gupta VK, PJM Carrott, R Singh & M Chaudhary (2016). Cellulose: a review as natural, modified and activated carbon adsorbent. Bioresour Technol 216, 1066 – 1076.

Kasirajan L, N Hoang, A Furtado, FC Botha & RJ Henry (2018). Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content. Sci Rep 8(1), 11612.

Khoo RZ, WS Chow & H Ismail (2018). Sugarcane bagasse fiber and its cellulose nanocrystals for polymer reinforcement and heavy metal adsorbent: a review. Cellulose 25, 4303 – 4330.

Liu L, K Shang-Guan, B Zhang, X Liu, M Yan, L Zhang, Y Shi, M Zhang, Q Qian & J Li (2013). Brittle Culm1, a COBRA-Like protein, functions in cellulose assembly through binding cellulose microfibrils. PLoS Genet 9(8), e1003704.

Mahmud MA & FR Anannya (2021). Sugarcane bagasse – A source of cellulosic fiber for diverse applications. Heliyon 7(8), e07771.

Meents MJ, Y Watanabe & AL Samuels. The cell biology of secondary cell wall biosynthesis. Ann Bot 121(6), 1107 – 1125.

Niu E, X Shang, C Cheng, J Bao, Y Zeng, C Cai, X Du & W Guo (2015). Comprehensive analysis of the COBRA-like (COBL) gene family in Gossypium identifies two COBLs potentially associated with fiber quality. PLoS ONE 10(12), e0145725.

Putranto RA, C Duan, Kuswanhadi, T Chaidamsari, M Rio, P Piyatrakul, E Herlinawati, J Pirrello, F Dessailly, & J Leclercq (2015). Ethylene response factors are controlled by multiple harvesting stresses in Hevea brasiliensis. PLoS ONE 10(4), e0123618.

Putranto RA, I Martiansyah & RT Saptari (2017). In silico identification and comparative analysis of Hevea brasiliensis COBRA gene family. Proceeding International Conference on Science and Engineering 1, 39–47.

Roudier F, AG Fernandez, M Fujita, R Himmelspach, GHH Borner, G Schindelman, S Song, TI Baskin, P Dupree & GO Wasteneys (2005). COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. Plant Cell 17(6), 1749 – 1763.

Roudier F, G Schindelman, R DeSalle, PN Benfey (2002). The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. Plant Physiol. 130(2), 538–548.

Schindelman G, A Morikami, J Jung, TI Baskin, NC Carpita, P Derbyshire, MC McCann & PN Benfey (2001). COBRA encodes a putative GPI-anchored protein, which is polarly localized and necessary for oriented cell expansion in arabidopsis. Genes Dev 15(9), 1115–1127.

Synytsya A & M Novak (2014). Structural analysis of glucans. Ann Transl Med 2(2), 17.

Takahashi D, Y Kawamura, M Uemura (2016). Cold acclimation is accompanied by complex responses of glycosylphosphatidylinositol (GPI)-anchored proteins in Arabidopsis. J Exp Bot 67(17), 5203–5215.

Thomas LH, VT Forsyth, A Sturcova, CJ Kennedy, RP May, CM Altaner, DC Apperley, TJ Wess & MC Jarvis (2013). Plant Physiol 161(1), 465 – 476.

Wsoo MA, S Shahir, SPM Bohari, NHM Nayan & SIA Razak (2020). A review on the properties of electrospun cellulose acetate and its application in drug delivery systems: A new prespective. Carbohydr Res 491, 107978.

Zhang W, W Qin, H Li & A Wu (2021). Biosynthesis and transport of nucleotide sugars for plant hemicellulose. Front Plant Sci 12, 723128.

Zhou K (2019). Glycosylphosphatidylinositol-anchored proteins in Arabidopsis and one of their common roles in signaling transduction. Front Plant Sci 10, 1022.

Zurzolo C & K Simons (2016). Glycosylphosphatidylinositol-anchored proteins: Membrane organization and transport. Biomembranes 1858(4), 632 – 639.








How to Cite

PUTRANTO, R. A., PERMATASARI, G. W., & SAPTARI, R. T. (2022). The in silico study of the COBRA gene family in sugarcane related to potential biomass content. Menara Perkebunan, 90(1).

Most read articles by the same author(s)

1 2 3 > >>