Abstract
Plastid terminal oxidase (PTOX) is a chloroplast enzyme that catalyzes oxidation of plastoquinol (PQH2) and reduction of molecular oxygen to water. Its function has been associated with carotenoid biosynthesis, chlororespiration and environmental stress responses in plants. In the majority of plant species, a single gene encodes the protein and little is known about events of PTOX gene duplication and their implication to plant metabolism. Previously, two putative PTOX (PTOX1 and 2) genes were identified in Glycine max, but the evolutionary origin and the specific function of each gene was not explored. Phylogenetic analyses revealed that this gene duplication occurred apparently during speciation involving the Glycine genus ancestor, an event absent in all other available plant leguminous genomes. Gene expression evaluated by RT-qPCR and RNA-seq data revealed that both PTOX genes are ubiquitously expressed in G. max tissues, but their mRNA levels varied during development and stress conditions. In development, PTOX1 was predominant in young tissues, while PTOX2 was more expressed in aged tissues. Under stress conditions, the PTOX transcripts varied according to stress severity, i.e., PTOX1 mRNA was prevalent under mild or moderate stresses while PTOX2 was predominant in drastic stresses. Despite the high identity between proteins (97%), molecular docking revealed that PTOX1 has higher affinity to substrate plastoquinol than PTOX2. Overall, our results indicate a functional relevance of this gene duplication in G. max metabolism, whereas PTOX1 could be associated with chloroplast effectiveness and PTOX2 to senescence and/or apoptosis.
Similar content being viewed by others
References
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Aluru MR, Bae H, Wu D, Rodermel SR (2001) The Arabidopsis immutans mutation affects plastid differentiation and the morphogenesis of white and green sectors in variegated plants. Plant Physiol 127:67–77
Araújo Castro J, Gomes Ferreira MD, Santana Silva RJ, Andrade BS, Micheli F (2017) Alternative oxidase (AOX) constitutes a small family of proteins in Citrus clementina and Citrus sinensis L. Osb PLoS One 12:e0176878. https://doi.org/10.1371/journal.pone.0176878
Balazadeh S, Riaño-Pachón DM, Mueller-Roeber B (2008) Transcription factors regulating leaf senescence in Arabidopsis thaliana. Plant Biol (Stuttg) 1:63–75
Belamkar V, Weeks NT, Bharti AK, Farmer AD, Graham MA, Cannon SB (2014) Comprehensive characterization and RNA-Seq profiling of the HD-zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. BMC Genomics 15:950. https://doi.org/10.1186/1471-2164-15-950
Berthold DA, Stenmark P (2003) Membrane-bound diiron carboxylate proteins. Annu Rev Plant Biol 54:497–517
Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araújo AC, Kozik A, Kim KD, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimarães PM, Isobe S, Guo B, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SC, Xun X, Jackson SA, Michelmore R, Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–446
Brown AV, Hudson KA (2015) Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons. BMC Plant Biol 15:169. https://doi.org/10.1186/s12870-015-0553-y
Burki F, Flegontov P, Oborník M, Cihlárˇ J, Pain A, Lukes J, Keeling PJ (2012) Re-evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin. Genome Biol Evol 4(6):626–635
Busch F, Hüner NP, Ensminger I (2008) Increased air temperature during simulated autumn conditions impairs photosynthetic electron transport between photosystem II and photosystem I. Plant Physiol 147:402–414
Carol P, Kuntz M (2001) A plastid terminal oxidase comes to light: implications for carotenoid biosynthesis and chlororespiration. Trends Plant Sci 6:31–36
Carol P, Stevenson D, Bisanz C, Breitenbach J, Sandmann G, Mache R, Coupland G, Kuntz M (1999) Mutations in the Arabidopsis gene IMMUTANS cause a variegated phenotype by inactivating a chloroplast terminal oxidase associated with phytoene desaturation. Plant Cell 11:57–68
Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nat Genet 31:415–418
Chang S, Thurber CS, Brown PJ, Hartmen GL, Lambert KN, Domier LL (2014) Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS One 9:1–9
Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21
Chen YA, Wen YC, Chang WC (2012) AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. BMC Genomics 13:85. https://doi.org/10.1186/1471-2164-13-85
Chow CN, Zheng HQ, Wu NY, Chien CH, Huang HD, Lee TY, Chiang-Hsieh YF, Hou PF, Yang TY, Chang WC (2015) PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. Nucleic Acids Res 44:D1154–D1160
Costa JH, McDonald AE, Arnholdt-Schmitt B, de Melo DF (2014) A classification scheme for alternative oxidases reveals the taxonomic distribution and evolutionary history of the enzyme in angiosperms. Mitochondrion 19:172–183
Costa JH, Saraiva KDC, Morais VD, Oliveira JTA, Sousa DOB, de Melo DF, Morais JKS, Vasconcelos IM (2016) Reference gene identification for real-time PCR analyses in soybean leaves under fungus (Cercospora kikuchii) infection and treatments with salicylic and jasmonic acids. Australasian Plant Pathol 45:191–199
Díaz M, de Haro V, Muñoz R, Quiles MJ (2007) Chlororespiration is involved in the adaptation of Brassica plants to heat and high light intensity. Plant Cell Environ 30:1578–1585
Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8:978–984
Fu A, Park S, Rodermel S (2005) Sequences required for the activity of PTOX (IMMUTANS), a plastid terminal oxidase in vitro and in planta mutagenesis of iron-binding sites and a conserved sequence that corresponds to exon 8. J Biol Chem 280:42489–42496
Gamboa J, Muñoz R, Quiles MJ (2009) Effects of antimycin a and n-propyl gallate on photosynthesis in sun and shade plants. Plant Sci 177:643–647
Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2012) Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Aust J Chem 4:17. https://doi.org/10.1186/1758-2946-4-17
Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8:R19. https://doi.org/10.1186/gb-2007-8-2-r19
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297–300
Hofmann K, Stoffel W (1993) TMbase - a database of membrane spanning proteins segments. Biol Chem Hoppe Seyler 374(166)
Hossain MS, ElSayed AI, Moore M, Dietz KJ (2017) Redox and reactive oxygen species network in acclimation for salinity tolerance in sugar beet. J Exp Bot 68:1283–1298
Hu R, Fan C, Li H, Zhang Q, Fu YF (2009) Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Mol Biol 10:93. https://doi.org/10.1186/1471-2199-10-93
Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G (2015) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31:1296–1297
Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202
Josse EM, Simkin AJ, Gaffé J, Labouré AM, Kuntz M, Carol P (2000) A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol 123:1427–1436
Josse EM, Alcaraz JP, Labouré AM, Kuntz M (2003) In vitro characterization of a plastid terminal oxidase (PTOX). FEBS J 270:3787–3794
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) The Phyre2 web portal for protein modelling, prediction and analysis. Nat Protoc 10:845–885
Kim DE, Chivian D, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32:526–5318
Kong J, Gong JM, Zhang ZG, Zhang JS, Chen SY (2003) A new AOX homologous gene OsIM1 from rice (Oryza sativa L.) with an alternative splicing mechanism under salt stress. Theor Appl Genet 107:326–331
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359
Lee WS, Fu SF, Li Z, Murphy AM, Dobson EA, Garland L, Chaluvadi SR, Lewsey MG, Nelson RS, Carr JP (2016) Salicylic acid treatment and expression of an RNA-dependent RNA polymerase 1 transgene inhibit lethal symptoms and meristem invasion during tobacco mosaic virus infection in Nicotiana benthamiana. BMC Plant Biol 16:15. https://doi.org/10.1186/s12870-016-0705-8
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325–327
Li YH, Zhou G, Ma J, Jiang W, Jin LG, Zhang Z, Guo Y, Zhang J, Sui Y, Zheng L, Zhang SS, Zuo Q, Shi XH, Li YF, Zhang WK, Hu Y, Kong G, Hong HL, Tan B, Song J, Liu ZX, Wang Y, Ruan H, Yeung CKL, Liu J, Wang H, Zhang LJ, Guan RX, Wang KJ, Li WB, Chen SY, Chang RZ, Jiang Z, Jackson SA, Li R, Q LJ (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32:1045–1052
Liu L, Zhou Y, Szczerba MW, Li X, Lin Y (2010) Identification and application of a rice senescence-associated promoter. Plant Physiol 153:1239–1249
Liu Q, Chang S, Hartman GL, Domier LL (2018) Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean. Plant J 95:71–85
Magalhães CS, Barbosa HJC, Dardenne LE (2004) Selection-insertion schemes in genetic algorithms for the flexible ligand docking problem. Lect Notes Comput Sci 3102:1–12
Magalhães CS, Almeida DM, Barbosa HJC, Dardenne LE (2014) A dynamic niching genetic algorithm strategy for docking of highly flexible ligands. Inf Sci 289:206–224
Marshall OJ (2004) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 20:2471–2472
McDonald AE, Vanlerberghe GC (2006) Origins, evolutionary history, and taxonomic distribution of alternative oxidase and plastoquinol terminal oxidase. Comp Biochem Physiol Part D Genomics Proteomics 1:357–364
McDonald AE, Ivanov AG, Bode R, Maxwell DP, Rodermel SR, Hüner NPA (2011) Flexibility in photosynthetic electron transport: the physiological role of plastoquinol terminal oxidase (PTOX). Biochim Biophys Acta 1807(8):954–967
Moretzsohn MC, Hopkins MS, Mitchell SE, Kresovich S, Valls JF, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 4:11. https://doi.org/10.1186/1471-2229-4-11
Muñoz R, Quiles MJ (2013) Water deficit and heat affect the tolerance to high illumination in Hibiscus plants. Int J Mol Sci 14:5432–5444
Nawrocki WJ, Tourasse NJ, Taly A, Rappaport F, Wollman FA (2015) The plastid terminal oxidase: its elusive function points to multiple contributions to plastid physiology. Annu Rev Plant Biol 66:49–74
Panchy N, Lehti-Shiu M, Shiu SH (2016) Evolution of gene duplication in plants. Plant Physiol 171:2294–2316
Paredes M, Quiles MJ (2013) Stimulation of chlororespiration by drought under heat and high illumination in Rosa meillandina. Plant Physiol 170:165–171
Rutledge RG, Stewart D (2008) Critical evaluation of methods used to determine amplification efficiency refutes the exponential character of real-time PCR. BMC Mol Biol 9:96. https://doi.org/10.1186/1471-2199-9-96
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sakai H, Aoyama T, Oka A (2000) Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Plant J 24:703–711
Saraiva KDC, de Melo DF, Morais VD, Vasconcelos IM, Costa JH (2014) Selection of suitable soybean EF1a genes as internal controls for real-time PCR analyses of tissues during plant development and under stress conditions. Plant Cell Rep 33:1453–1465
Saraiva KDC, Oliveira AER, dos Santos CP, Lima KTL, de Sousa JM, de Melo DF, Costa JH (2016) Phylogenetic analysis and differential expression of EF1α genes in soybean during development, stress and phytohormone treatments. Mol Gen Genomics 291:1505–1522
Savitch LV, Ivanov AG, Krol M, Sprott DP, Oquist G, Huner NP (2010) Regulation of energy partitioning and alternative electron transport pathways during cold acclimation of lodgepole pine is oxygen dependent. Plant Cell Physiol 51:1555–1570
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
Schrödinger LLC (2017) The PyMOL molecular graphics system, Version 18
Schrödinger Release (2017) MS jaguar, Schrödinger, LLC, New York, NY, 2017 maestro version 111012. MMshare Version 37012
Shiba T, Kido Y, Sakamoto K, Inaoka DK, Tsuge C, Tatsumi R, Takahashi G, Balogun EO, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Saimoto H, Moore AL, Harada S, Kita K (2013) Structure of the trypanosome cyanide-insensitive alternative oxidase. Proc Natl Acad Sci U S A 110:4580–4585
Shin JH, Vaughn JN, Abdel-Haleem H, Chavarro C, Abernathy B, Kim KD, Jackson SA, Li Z (2015) Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance. BMC Plant Biol 15:26. https://doi.org/10.1186/s12870-015-0422-8
Shirsat A, Wilford N, Croy R, Boulter D (1989) Sequences responsible for the tissue specific promoter activity of a pea legumin gene in tobacco. Mol Gen Genet 215:326–331
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Mol Syst Biol 7:539. https://doi.org/10.1038/msb.2011.75
Sun X, Wen T (2011) Physiological roles of plastid terminal oxidase in plant stress responses. J Biosci 36:951–956
Sun X, Yang CQ, Wen T, Zeng FC, Wang Q, Yang WY, Lin HH (2014) Water stress enhances expression of genes encoding plastid terminal oxidase and key components of chlororespiration and alternative respiration in soybean seedlings. Z Naturforsch C 69:300–308
Sun X, Lei T, Du JB, Yang WY (2015) Identification and characterization of two paralogous plastid terminal oxidase genes in soybean. Int J Agric Biol 17:1275–1278
Tallón C, Quiles MJ (2007) Acclimation to heat and high light intensity during the development of oat leaves increases the NADH DH complex and PTOX levels in chloroplasts. Plant Sci 173:438–445
Tang Y, Sun X, Wen T, Liu M, Yang M, Chen X (2017) Implications of terminal oxidase function in regulation of salicylic acid on soybean seedling photosynthetic performance under water stress. Plant Physiol Biochem 112:19–28
Teakle GR, Manfield IW, Graham JF, Gilmartin PM (2002) Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics. Plant Mol Biol 50:43–57
Thiers KLL, da Silva JHM, Sartori GR, dos Santos CP, Saraiva KDC, Roque ALM, Arnholdt-Schmitt B, Costa JH (2019) Polymorphisms in plastoquinol oxidase (PTOX) from Arabidopsis accessions indicate SNP-induced structural variants associated with altitude and rainfall. J Bioenerg Biomembr 51:151–164. https://doi.org/10.1007/s10863-018-9784-6
Thomas H, Ougham H, Mur L, Jansson S (2015) Senescence and cell death. In: Buchanan BB, Gruissem W, Jones RL (eds) Biochemistry & Molecular Biology of plants, 2nd edn. Wiley Blackwell, Oxford, pp 925–952
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc 7:562–578
Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461
Tyczewska A, Gracz J, Kuczyński J, Twardowski T (2016) Deciphering soybean molecular stress response via high-throughput approach. Acta Biochim Pol 63:631–643
Villain P, Mache R, Zhou DX (1996) The mechanism of GT element-mediated cell type-specific transcriptional control. J Biol Chem 271:32593–32598
Wang J, Sommerfeld M, Hu Q (2009) Occurrence and environmental stress responses of two plastid terminal oxidases in Haematococcus pluvialis (Chlorophyceae). Planta 230:191–203
Wang Y, Wang X, Tang H, Tan X, Ficklin SP, Feltus FA, Paterson AH (2011) Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One 6:e28150. https://doi.org/10.1371/journal.pone.0028150
Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics 54:5.6.1–5.6.37. https://doi.org/10.1002/cpbi.3
Yanagisawa S, Schmidt RJ (1999) Diversity and similarity among recognition sequences of Dof transcription factors. Plant J 17:209–214
Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273
Acknowledgments
The authors gratefully thank the National Council for Scientific and Technological Development for financial support (CNPq, grant 455327/2014-9). Maia RA, Thiers KLL and Santos CP were supported by master and doctoral grants from CNPq. Roque ALM and Feijó DF were supported by master and post-doctoral grants from Council for Advanced Professional Training (CAPES), respectively. Costa JH received support from CNPq through Researcher fellowship (CNPq grant 309795/2017-6).
Author contribution statement
Maia RA and Saraiva KDC conducted the RT- qPCR experiments, Maia RA, Roque ALM, Feijó DF and Santos CP interpreted the experimental and in silico data, Thiers KLL and Silva JHM realized the molecular docking. Maia RA, Costa JH, Feijó DF and Arnholdt-Schmitt B designed the study and wrote the manuscript (with input from all authors). All authors read and approved the final version of the paper.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interests
The authors declare that have no conflict of interest.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Maia, R.A., da Cruz Saraiva, K.D., Roque, A.L.M. et al. Differential expression of recently duplicated PTOX genes in Glycine max during plant development and stress conditions. J Bioenerg Biomembr 51, 355–370 (2019). https://doi.org/10.1007/s10863-019-09810-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10863-019-09810-x