In silico characterization and comparison of the fruit ripening related beta‐ amylase (BAM) gene family in banana genome A and B

Erdianty Setiabudi; Karlia Meitha; Fenny Martha Dwivany

doi:10.22146/ijbiotech.65142

In silico characterization and comparison of the fruit ripening related beta‐ amylase (BAM) gene family in banana genome A and B

https://doi.org/10.22146/ijbiotech.65142

Erdianty Setiabudi⁽¹⁾, Karlia Meitha⁽²⁾, Fenny Martha Dwivany^(3*)

(1) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung 40132, Indonesia
(2) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung 40132, Indonesia; Indonesia Biodiversity and Biogeography Research Institute (INABIG), Jl. Cimanuk 6, Bandung 40132, Indonesia
(3) School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung 40132, Indonesia; Indonesia Biodiversity and Biogeography Research Institute (INABIG), Jl. Cimanuk 6, Bandung 40132, Indonesia; Bioscience and Biotechnology Research Center, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung 40132, Indonesia
(*) Corresponding Author

Abstract

Banana is one of the most important commodities for maintaining global food security. Primary metabolic processes during the ripening of banana greatly affect post‐harvest quality, particularly in starch metabolism. The beta‐ amylase (BAM) gene family is known as a group of genes that plays an important role in starch metabolism regulation. In this study, we focused on the characterization and comparative analysis of the BAM gene family in DH Pahang and Pisang Klutuk Wulung (PKW) varieties, these being the AA and BB genomes, respectively. The sequences of BAM gene family were retrieved from the database of Musa acuminata ’DH Pahang’ and Musa balbisiana ’PKW’ genome, then structural and functional characterization was performed, followed by identification of cis‐acting elements in the BAM promoter regions. The results showed that the BAM gene family structure was relatively conserved in both genomes, and a putative BAM11 gene was found, the function of which has not been studied in other plants. Cis‐acting element analysis showed that they were distinct in the copy number and types of elements that were responsive to various phytohormones. This study suggested that the BAM genes involved in ripening are spatiotemporally regulated. However, further functional genomic analysis is required to describe the specific role and regulation of BAM genes during ripening in banana.

Keywords

A and B genome; BAM; Banana; Fruit Ripening

Full Text:

PDF

References

Bailey T, Johnson J, Grant C, Noble W. 2015. The MEME Suite. Nucleic Acids Res. 43(W1). doi:10.1093/nar/gkv416.

Biłas R, Szafran K, HnatuszkoKonka K, Kononowicz A. 2016. Cisregulatory elements used to control gene expression in plants. Plant Cell, Tissue Organ Cult. 127(2):269–287. doi:10.1007/s1124001610577.

Clark K, KarschMizrachi I, Lipman D, Ostell J, Sayers E. 2016. GenBank. Nucleic Acids Res. 44(D1):67– 72. doi:10.1007/s1124001610577.

CordenunsiLysenko B, Nascimento J, CastroAlves V, Purgatto E, Fabi J, PeroniOkita F. 2019. The Starch Is (Not) Just Another Brick in the Wall: The Primary Metabolism of Sugars During Banana Ripening. Front Plant Sci. 10. doi:10.3389/fpls.2019.00391.

Davey M, Gudimella R, Harikrishna J, Sin L, Khalid N, Keulemans J. 2013. A draft Musa balbisiana genome sequence for molecular genetics in polyploid, interand intraspecific Musa hybrids. BMC Genomics. 14(1):683. doi:10.1186/1471216414683.

D’hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, et al. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217. doi:10.1038/nature11241.

Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Bocs S. 2013. The Banana Genome Hub. Database. doi:10.1093/database/bat035.

Dwivany F, Hermawaty D, Esyanti R. 2016. Raja Bulu’ Banana MaACS1 and MaACO1 Gene Expression during Postharvest Storage. Acta Hortic. p. 111–114. doi:10.17660/actahortic.2016.1120.16.

Edgar R. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797. doi:10.1093/nar/gkh340.

FAO. 2020. Mediumterm Outlook: Prospects for global production and trade in bananas and tropical fruits 2019 to 2028. Rome: Food and Agriculture Organization of the United Nations.

Hall T. 1999. BioEdit: A userfriendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95–98.

Hu B, Jin J, Guo A, Zhang H, Luo J, Gao G. 2015. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics. 31(8):1296–1297. doi:10.1093/bioinformatics/btu817.

Johnson X, Wostrikoff K, Finazzi G, Kuras R, Schwarz C, Bujaldon S, Vallon O. 2010. MRL1, a Conserved Pentatricopeptide Repeat Protein, Is Required for Stabilization of rbcL mRNA in Chlamydomonas and Arabidopsis. The Plant Cell. 22(1):234–248. doi:10.1105/tpc.109.066266.

Jourda C, Cardi C, Gibert O, Toro AG, Ricci J, Mbéguié AMbéguié D, Yahiaoui N. 2016. Lineagespecific evolutionary histories and regulation of major starch metabolism genes during banana ripening. Front Plant Sci. 7. doi:10.3389/fpls.2016.01778.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 35(6):1547–1549. doi:10.1093/molbev/msy096.

Larotonda F, Genena A, Dantela D, Soares H, Laurindo J, Moreira R, Ferreira S. 2008. Study of banana (Musa aaa Cavendish cv Nanica) trigger ripening for small scale process. Braz Arch Biol Technol. 51(5):1033– 1047. doi:10.1590/s151689132008000500021.

Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Peer Y, Rombauts S. 2002. PlantCARE, a database of plant cisacting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30(1):325–327. doi:10.1093/nar/30.1.325.

Lu S, Wang J, Chitsaz F, Derbyshire M, Geer R, Gonzales N, MarchlerBauer A. 2020. CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Res. 48(D1). doi:10.1093/nar/gkz991.

Madeira F, Park Y, Lee J, Buso N, Gur T, Madhusoodanan N, Lopez R. 2019. The EMBLEBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47(W1). doi:10.1093/nar/gkz268.

Miao H, Sun P, Miao Y, Liu J, Zhang J, Jia C, Xu B. 2016. Genomewide identification and expression analysis of the βamylase genes strongly associated with fruit development, ripening, and abiotic stress response in two banana cultivars. FASE. 3(4):346. doi:10.15302/jfase2016127.

Mikami B, Degano M, Hehre E, Sacchettini J. 1994. Crystal structures of soybean bamylase reacted with bmaltose and maltal: active site components and their apparent roles in catalysis. Biochemistry. 33:7779–7787. doi:10.1021/bi00191a005.

Mitchell A, Attwood T, Babbitt P, Blum M, Bork P, Bridge A, Finn R. 2019. InterPro in 2019: Improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47(D1). doi:10.1093/nar/gky1100.

Monroe J, Pope L, Breault J, Berndsen C, Storm A. 2018. Quaternary structure, salt sensitivity, and allosteric regulation of βAMYLASE2 from Arabidopsis thaliana. Front Plant Sci. 9. doi:10.3389/fpls.2018.01176. URL https://doi.org/ 10.3389/fpls.2018.01176.

Monroe J, Storm A. 2018. Review: The Arabidopsis βamylase (BAM) gene family: Diversity of form and function. Plant Sci. 276:163–170. doi:10.1016/j.plantsci.2018.08.016.

Nascimento J, Júnior A, Bassinello P, Cordenunsi B, Mainardi J, E P. 2006. Betaamylase expression and starch degradation during banana ripening. Postharvest Biol Technol. 40. doi:10.1016/j.postharvbio.2005.11.008.

OECD. 2010. Safety Assessment of Transgenic Organisms, Volume 4. Harmonisation of Regulatory Oversight in Biotechnology. doi:10.1787/9789264096158en.

Pathak S, Sriramulu S, Thandavan S, Jothimani G, Banerjee A, Marotta F. 2018. Enhancement of shelf life of the climacteric fruits: a review on application of CRISPRi technology. Trends Tech Sci Res. 1(2).

Reinhold H, Soyk S, Simková K, Hostettler C, Marafino J, Mainiero S, Vaughan CK, Monroe JD, Zeeman SC. 2011. ΒAmylaseLike Proteins Function As Transcription Factors in Arabidopsis, Controlling Shoot Growth and Development. Plant Cell. 23(4):1391– 1403. doi:10.1105/tpc.110.081950.

Shan W, Guo Y, Wei W, Chen J, Lu W, Yuan D, Kuang J. 2019. Banana MaBZR1/2 associate with MaMPK14 to modulate cell wall modifying genes during fruit ripening. Plant Cell Rep. 39(1):35–46. doi:10.1007/s00299019024715.

Solovyev V, Kosarev P, Seledsov I, Vorobyev D. 2006. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 7(Suppl 1). doi:10.1186/gb20067s1s10.

Xiao Y, Kuang J, Qi X, Ye Y, Wu Z, Chen J, Lu W. 2018. A comprehensive investigation of starch degradation process and identification of a transcriptional activator MabHLH6 during banana fruit ripening. Plant Biotechnol J. 16(1):151–164. doi:10.1111/pbi.12756.

Xiong J. 2006. Essential bioinformatics. Cambridge: Cambridge University Press.

DOI: https://doi.org/10.22146/ijbiotech.65142