TY - GEN
T1 - Bioinformatics Study of Starch Synthase (SS) Gene Variation in Cassava (Manihot Esculenta) and Its Potential Use
AU - Hartati, N. Sri
AU - Ramadhani, Dini Viandi
AU - Desmawati, Iska
AU - Harmoko, Rikno
AU - Sudarmonowati, Enny
N1 - Publisher Copyright:
© 2023 American Institute of Physics Inc.. All rights reserved.
PY - 2023/1/4
Y1 - 2023/1/4
N2 - The starch synthase (SS) gene is one of the genes involved in the starch biosynthetic pathway. The expression level of SS regulates the starch quality and quantity in cassava. Therefore, the characteristics of SS in terms of nucleotide variations and its protein structure need to be identified using bioinformatics tools as the initial step to develop a cassava improvement strategy in the future. The nucleotides length and phylogenetic tree were constructed based on SS sequences of Manihot esculenta, Ipomea batatas and Solanum tuberosum showed low SS nucleotide variation. Characteristics of the motif and protein domain of starch synthase are derived from Glycosyltransferase 5 and 1 in Rossmann fold protein motifs. Characteristics of the secondary structure of starch synthase subunits comprised of the alpha helix, extended strand, and random coil structures. The starch synthase subunits of cassava tubers have predicted secondary structures ranging from 173-524 alpha-helix, 83-161 beta-sheet, and 321-574 random coil. The identity of the starch synthase subunit sequences of cassava is considerably high, with a similarity index of 50-82% compared to the homolog structure template. The identified physicochemical characteristics were instability index, aliphatic index, and GRAVY which all indexes showed varying values.
AB - The starch synthase (SS) gene is one of the genes involved in the starch biosynthetic pathway. The expression level of SS regulates the starch quality and quantity in cassava. Therefore, the characteristics of SS in terms of nucleotide variations and its protein structure need to be identified using bioinformatics tools as the initial step to develop a cassava improvement strategy in the future. The nucleotides length and phylogenetic tree were constructed based on SS sequences of Manihot esculenta, Ipomea batatas and Solanum tuberosum showed low SS nucleotide variation. Characteristics of the motif and protein domain of starch synthase are derived from Glycosyltransferase 5 and 1 in Rossmann fold protein motifs. Characteristics of the secondary structure of starch synthase subunits comprised of the alpha helix, extended strand, and random coil structures. The starch synthase subunits of cassava tubers have predicted secondary structures ranging from 173-524 alpha-helix, 83-161 beta-sheet, and 321-574 random coil. The identity of the starch synthase subunit sequences of cassava is considerably high, with a similarity index of 50-82% compared to the homolog structure template. The identified physicochemical characteristics were instability index, aliphatic index, and GRAVY which all indexes showed varying values.
UR - http://www.scopus.com/inward/record.url?scp=85146515176&partnerID=8YFLogxK
U2 - 10.1063/5.0119245
DO - 10.1063/5.0119245
M3 - Conference contribution
AN - SCOPUS:85146515176
T3 - AIP Conference Proceedings
BT - Proceedings of the 8th International Symposium of Innovative Bioproduction Indonesia on Biotechnology and Bioengineering 2021
A2 - Harmoko, Rikno
A2 - Nuryana, Isa
A2 - Izzati, Fauzia Nurul
A2 - Sawono, Ki Ageng
A2 - Khaerunnisa, Isyana
A2 - Rahmawati, Siti Irma
A2 - Bayu, Asep
A2 - Martin, Andri Fadillah
A2 - Hertati, Ai
A2 - Subandiyah, Siti
A2 - Sawitri, Widhi Dyah
PB - American Institute of Physics Inc.
T2 - 8th International Symposium of Innovative Bioproduction Indonesia on Biotechnology and Bioengineering: Global Platform on Biodiversity and Biotechnology, ISIBio 2021
Y2 - 15 November 2021 through 16 November 2021
ER -