De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L.

Yıl 2022, Cilt: 10 Sayı: 1, 285 - 299, 31.01.2022

Ercan Selçuk Ünlü , Gülgez Gökçe Yıldız

https://doi.org/10.29130/dubited.914845

Öz

Water lilies are aquatic, ornamental and economically valuable plants classified under Nymphaea genus. Nymphaea alba L., white water lily, has a special focus since it is a member of basal angiosperms. Alternative oxidase (AOX) proteins are the terminal oxidases in the electron transport chain of plants. Identification of alternative oxidase encoding genes for basal angiosperms is important to increase the quality of phylogenetic studies. However, AOX encoding genes were yet to be discovered for N. alba. In this study, we aimed to identify alternative oxidase encoding genes in N. alba by performing transcriptome analysis. Annotation of 272,934 unigenes with Trinotate tool revealed 77 transcripts with AOX domains characterized in known alternative oxidases. Blast analysis of these 77 sequences with known AOX proteins revealed three distinct AOX genes (AOX1, AOX2 and AOX4) in N. alba. After in silico subcellular localization analysis of three identified AOX proteins, AOX1, AOX2 are predicted as mitochondrial while AOX4 is a plastidic alternative oxidase protein. Template-based structural modeling results showed that all identified proteins are statistically similar to known structure models of corresponding AOXs.

Anahtar Kelimeler

AOX, Abant Lake, RNA-Seq, Water lilies

Destekleyen Kurum

Bolu Abant İzzet Baysal Üniversitesi

Proje Numarası

2014.03.03.714

Teşekkür

This study was financially supported by Bolu Abant İzzet Baysal University [Grant no: 2014.03.03.714]. We also thank Ph.D. students Özge KAYA, Ömer Can ÜNÜVAR, and Yunus ŞAHİN for helping through field sampling

De Novo Transkriptom Birleştirme Analizi Nymphaea alba L. Türünde Üç Alternatif Oksidaz Kodlayan Gen Olduğunu Göstermektedir

Öz

Nilüfer bitkileri ekonomik değeri yüksek sucul süs bitkileri olup Nymphaea ailesi altında sınıflandırılmaktadırlar. Nymphaea alba L. (Beyaz nilüfer) bazal angiospermlerin bir üyesi olduklarından özel bir öneme sahiptir. Alternatif oksidaz kodlayan genlerin bazal angiospermlerde belirlenmesi filogenetik çalışmaların kalitesini artırmak için önemlidir. N. alba için AOX sentezinden sorumlu genler henüz tanımlanmamıştır. Bu çalışmada transkriptom analizi uygulamaları ile N. alba türünde AOX sentezinden sorumlu genlerin tanımlanmasını amaçlanmıştır. Trinotate aracılığı ile 272934 unigenin tanımlaması yapılarak, bilinen alternatif oksidazlarda karakterize edilmiş AOX domainlerini içeren 77 transkriptin dizisi ortaya çıkarılmıştır. Bu 77 transkriptin bilinen AOX proteinlerine karşı Blast analizleri ile N. alba türüne ait üç ayrı AOX geni (AOX1, AOX2 and AOX4) tespit edilmiştir. In silico hücre içi lokalizasyon analizine göre AOX1 ve AOX2 proteinleri mitokondriyal, AOX4 ise plastidik alternatif oksidaz proteinidir. Şablon bazlı yapısal modelleme sonuçları, tanımlanmış bu proteinlerin model verilerinin, başka türlerde karşılık geldiği AOX proteinlerinin bilinen yapı modellerine istatistiksel olarak benzer olduğunu göstermiştir.

Anahtar Kelimeler

AOX, Abant Gölü, RNA-Seq, Nilüfergiller

Proje Numarası

2014.03.03.714

Kaynakça

• [1] H. Luo et al., “The expression of floral organ identity genes in contrasting water lily cultivars,” Plant Cell Rep., vol. 30, no. 10, pp. 1909–1918, 2011.
• [2] B. S. Thippeswamy, B. Mishra, V. P. Veerapur, and G. Gupta, “Anxiolytic activity of Nymphaea alba Linn. in mice as experimental models of anxiety,” Indian J. Pharmacol., vol. 43, no. 1, pp. 50–55, 2011.
• [3] N. Khan and S. Sultana, “Inhibition of potassium bromate-induced renal oxidative stress and hyperproliferative response by Nymphaea alba in Wistar rats,” J. Enzyme Inhib. Med. Chem., vol. 20, no. 3, pp. 275–283, 2005.
• [4] N. Khan and S. Sultana, “Anticarcinogenic effect of Nymphaea alba against oxidative damage, hyperproliferative response and renal carcinogenesis in Wistar rats,” Mol. Cell. Biochem., vol. 271, no. 1–2, pp. 1–11, 2005.
• [5] A. Chaveerach, T. Tanee, and R. Sudmoon, “Molecular identification and barcodes for the genus Nymphaea,” Acta Biol. Hung., vol. 62, no. 3, pp. 328–340, 2011.
• [6] D. E. . Soltis et al., “Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences,” Bot. J. Linn. Soc., vol. 133, no. 4, pp. 381–461, 2000.
• [7] P. Lakshmanan, “In vitro establishment and multiplication of Nymphaea hybrid  'James Brydon',” Plant Cell. Tissue Organ Cult., vol. 36, no. 1, pp. 145–148, 1994.
• [8] R. Clifton, A. H. Millar, and J. Whelan, “Alternative oxidases in Arabidopsis: a comparative analysis of differential expression in the gene family provides new insights into function of non-phosphorylating bypasses.,” Biochim. Biophys. Acta, vol. 1757, no. 7, pp. 730–41, 2006.
• [9] B. H. Simons, F. F. Millenaar, L. Mulder, L. C. Van Loon, and H. Lambers, “Enhanced Expression and Activation of the Alternative Oxidase during Infection of Arabidopsis withPseudomonas syringae pv tomato,” Plant Physiol., vol. 120, no. 2, 1999.
• [10] C.-R. Li et al., “Unravelling mitochondrial retrograde regulation in the abiotic stress induction of rice ALTERNATIVE OXIDASE 1 genes,” Plant. Cell Environ., vol. 36, no. 4, pp. 775–788, 2013.
• [11] D. A. Berthold and P. Stenmark, “Membrane-bound diiron carboxylate proteins,” Annu. Rev. Plant Biol., vol. 54, no. 1, pp. 497–517, 2003.
• [12] A. E. McDonald and G. C. Vanlerberghe, “Origins, evolutionary history, and taxonomic distribution of alternative oxidase and plastoquinol terminal oxidase,” Comp. Biochem. Physiol. - Part D Genomics Proteomics, vol. 1, no. 3, pp. 357-364, 2006.
• [13] R. Pennisi, D. Salvi, V. Brandi, R. Angelini, P. Ascenzi, and F. Polticelli, “Molecular Evolution of Alternative Oxidase Proteins: A Phylogenetic and Structure Modeling Approach,” J. Mol. Evol., vol. 82, no. 4-5, pp. 207-218, 2016.
• [14] J. N. Siedow and A. L. Umbach, “The mitochondrial cyanide-resistant oxidase: structural conservation amid regulatory diversity,” Biochim. Biophys. Acta - Bioenerg., vol. 1459, no. 2, pp. 432–439, 2000.
• [15] A. L. Umbach, F. Fiorani, and J. N. Siedow, “Characterization of Transformed Arabidopsis with Altered Alternative Oxidase Levels and Analysis of Effects on Reactive Oxygen Species in Tissue,” Plant Physiol., vol. 139, no. 4, pp. 1806-1820, 2005.
• [16] D. P. Maxwell, Y. Wang, and L. McIntosh, “The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells.,” Proc. Natl. Acad. Sci. U. S. A., vol. 96, no. 14, pp. 8271–6, 1999.
• [17] M. Ribas-Carbo, R. Aroca, M. A. Gonzàlez-Meler, J. J. Irigoyen, and M. Sánchez-Dı́az, “The Electron Partitioning between the Cytochrome and Alternative Respiratory Pathways during Chilling Recovery in Two Cultivars of Maize Differing in Chilling Sensitivity,” Plant Physiol., vol. 122, no. 1, pp. 199–204, 2000.
• [18] T.-T. Chai, D. Simmonds, D. A. Day, T. D. Colmer, and P. M. Finnegan, “A GmAOX2b antisense gene compromises vegetative growth and seed production in soybean,” Planta, vol. 236, no. 1, pp. 199–207, 2012.
• [19] H. Jiang, R. Lei, S.-W. Ding, and S. Zhu, “Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads,” BMC Bioinformatics, vol. 15, no. 1, p. 182, 2014.
• [20] B. J. Haas et al., “De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.,” Nat. Protoc., vol. 8, no. 8, pp. 1494–512, 2013.
• [21] C. Trapnell and S. L. Salzberg, “How to map billions of short reads onto genomes.,” Nat. Biotechnol., vol. 27, no. 5, pp. 455–457, 2009.
• [22] R. M. Waterhouse et al., “BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.,” Mol. Biol. Evol., vol. 35, no. 3, pp. 543–548, 2018.
• [23] J. E. Stajich et al., “The Bioperl toolkit: Perl modules for the life sciences.,” Genome Res., vol. 12, no. 10, pp. 1611–8, 2002.
• [24] F. Sievers et al., “Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.,” Mol. Syst. Biol., vol. 7, p. 539, 2011.
• [25] A. M. Waterhouse, J. B. Procter, D. M. A. Martin, M. Clamp, and G. J. Barton, “Jalview Version 2--a multiple sequence alignment editor and analysis workbench.,” Bioinformatics, vol. 25, no. 9, pp. 1189–91, 2009.
• [26] O. Emanuelsson, H. Nielsen, S. Brunak, and G. von Heijne, “Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence,” J. Mol. Biol., vol. 300, no. 4, pp. 1005–1016, 2000.
• [27] M. G. Claros and P. Vincens, “Computational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences,” Eur. J. Biochem., vol. 241, no. 3, pp. 779–786, 1996.
• [28] J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Res., vol. 22, no. 22, pp. 4673-4680, 1994.
• [29] M. N. Price, P. S. Dehal, and A. P. Arkin, “Fasttree: Computing large minimum evolution trees with profiles instead of a distance matrix,” Mol. Biol. Evol., vol. 26, no. 7, pp. 1641- 1650, 2009.
• [30] M. Källberg et al., “Template-based protein structure modeling using the RaptorX web server.,” Nat. Protoc., vol. 7, no. 8, pp. 1511–22, 2012.
• [31] A. E. McDonald, “Alternative oxidase: an inter-kingdom perspective on the function and regulation of this broadly distributed ‘cyanide-resistant’ terminal oxidase,” Funct. Plant Biol., vol. 35, no. 7, p. 535, 2008.
• [32] B. B. Patnaik et al., “Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery,” PLoS One, vol. 11, no. 2, p. e0148622, 2016.
• [33] J. Pellicer, L. J. Kelly, C. Magdalena, and I. J. Leitch, “Insights into the dynamics of genome size and chromosome evolution in the early diverging angiosperm lineage Nymphaeales (water lilies).,” Genome, vol. 56, no. 8, pp. 437–449, 2013.
• [34] R. Ming et al., “Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.),” Genome Biol., vol. 14, no. R41, pp. 1-11, 2013.
• [35] M. E. Bolger, B. Arsova, and B. Usadel, “Plant genome and transcriptome annotations: from misconceptions to simple solutions,” Brief. Bioinform., vol. 12, p. bbw135, 2017.
• [36] N. J. B. Brereton et al., “Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants.,” Plant Physiol., vol. 171, no. 1, pp. 3–24, 2016.
• [37] J. Whelan, A. H. Millar, and D. A. Day, “The alternative oxidase is encoded in a multigene family in soybean,” Planta, vol. 198, no. 2, pp. 197–201, 1996.
• [38] Y. Ito, D. Saisho, M. Nakazono, N. Tsutsumi, and A. Hirai, “Transcript levels of tandem-arranged alternative oxidase genes in rice are increased by low temperature,” Gene, vol. 203, no. 2, pp. 121–129, 1997.
• [39] D. Saisho, E. Nambara, S. Naito, N. Tsutsumi, A. Hirai, and M. Nakazono, “Characterization of the gene family for alternative oxidase from Arabidopsis thaliana,” Plant Mol. Biol., vol. 35, no. 5, pp. 585–596, 1997.
• [40] T. Magnani et al., “Cloning and functional expression of the mitochondrial alternative oxidase of Aspergillus fumigatus and its induction by oxidative stress,” FEMS Microbiol. Lett., vol. 271, no. 2, pp. 230–238, 2007.
• [41] J. N. Siedow, A. L. Umbach, and A. L. Moore, “The active site of the cyanide-resistant oxidase from plant mitochondria contains a binuclear iron center,” FEBS Lett., vol. 362, no. 1, pp. 10–14, 1995.
• [42] D. A. Berthold, M. E. Andersson, and P. Nordlund, “New insight into the structure and function of the alternative oxidase,” Biochim. Biophys. Acta - Bioenerg., vol. 1460, no. 2–3, pp. 241–254, 2000.
• [43] V. V Goremykin, K. I. Hirsch-Ernst, S. Wölfl, and F. H. Hellwig, “The Chloroplast Genome of Nymphaea alba: Whole-Genome Analyses and the Problem of Identifying the Most Basal Angiosperm,” Mol. Biol. Evol., vol. 21, no. 7, pp. 1445–1454, 2004.
• [44] J. Peng and J. Xu, “Raptorx: Exploiting structure information for protein alignment by statistical inference,” Proteins Struct. Funct. Bioinforma., vol. 79, no. S10, pp. 161–171, 2011.