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Transcriptome-wide identification of genes involved in Ascorbate–Glutathione cycle (Halliwell–Asada pathway) and related pathway for elucidating its role in antioxidative potential in finger millet (Eleusine coracana (L.))

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Abstract

Finger millet is being recognized as a potential future crop due to their nutrient contents and antioxidative properties, which are much higher compared to the other minor millets for providing health benefits. The synthesis of these nutritional components is governed by the expression of several gene(s). Therefore, it is necessary to characterize these genes for understanding the molecular mechanisms behind de novo synthesis of nutrient components. Apart from this, these important compounds could also serve as candidate genes for imparting stress tolerance in other crop plants also. In the present study, effort has been made to identify genes involved in Ascorbate–Glutathione cycle (Halliwell–Asada Pathway) and related pathway genes for elucidating its role in antioxidative potential mechanism through transcriptome data analysis. APX, DHAR, MDHAR, GR, and SOD have been identified as the key genes of the pathway in two genotypes GP-1 (low Ca2+) and GP-45 (high Ca2+) of finger millet with reference to rice as a model system, besides, 30 putatively expressed genes/proteins were also investigated. Furthermore, the sequences of identified genes were analyzed systematically; gene ontology (GO) annotation and enrichment analysis of assembled unitranscripts were also performed using Blast2GO. As a result, 49 GO terms, 5 Enzyme Commission (EC) numbers, and 2 KEGG pathway maps were generated. GO results revealed that these genes are mainly involved in two biological processes (BP), viz., oxidation–reduction process (GO:0055114) and cellular oxidant detoxification (GO:0098869), and showed oxidoreductase activity (GO:0016491). KEGG analysis showed that APX, DHAR, MDHAR, and GR are directly connected to biosynthetic pathways of secondary metabolites, mainly polyphenolic compounds (flavonoid, tannin, and lignin) involved in glutathione metabolism (KEGG:00480) and ascorbate and aldarate metabolism (KEGG:00053). While SOD, is indirectly connected and also has significant medicinal attributes and antioxidant properties. Moreover, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were also calculated for expression analysis and found that the FPKM values of genes present in GP-1 are higher than that of GP-45. Thus, GP-1 genotype was found to have higher stress regulated gene expression in comparison to GP-45. Taken together, the present transcriptome-based investigation unlocks new avenues for systematic functional analysis of novel ROS scavenging candidate genes that could be effectively applied for improvising human health and nutrition.

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Change history

  • 19 August 2019

    In the original publication the text “ROS-producing” genes in the entire article should be replaced by “ROS-scavenging” genes. We regret the inconvenience caused.

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  Google Scholar 

  • Anthony U, Mosses LG, Chandra TS (1998) Inhibition of Salmonella typhimurium and Escherichia coli by fermented flour of finger millet (Eleusine coracana). World J Microbiol Biotechnol 14:883–886

    Article  Google Scholar 

  • Avashthi H, Jha R, Sharma M, Yadav AK, Mishra AK, Ramteke PW, Kumar A (2017) Artificial neural networks (ANNs) Approach for classification of seed storage proteins of various nutritionally superior cereal crops. Int J Agricu Sci 9:3749–3751

    Google Scholar 

  • Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37(Web Server issue):W202–W208. https://doi.org/10.1093/nar/gkp335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bowler C, Montagu MV, Inze D (1992) Superoxide dismutase and stress tolerance. Annu Rev Plant Physiol Plant Mol Biol 43:83–116

    Article  CAS  Google Scholar 

  • Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A (2007) GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol 8(1):R3. https://doi.org/10.1186/gb-2007-8-1-r3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chandrasekara A, Shahidi F (2010) Content of insoluble bound phenolics in millets and their contribution to antioxidant capacity. J Agric Food Chem 58:6706–6714

    Article  CAS  Google Scholar 

  • Chandrasekara A, Shahidi F (2011a) Antiproliferative potential and DNA scission inhibitory activity of phenolics from whole millet grains. J Funct Foods 3:159–170

    Article  CAS  Google Scholar 

  • Chandrasekara A, Shahidi F (2011b) Inhibitory activities of soluble and bound millet seed phenolics on free radicals and reactive oxygen species. J Agric Food Chem 59:428–436

    Article  CAS  Google Scholar 

  • Chethan S, Malleshi NG (2007) Finger millet polyphenols: characterization and their nutraceutical potential. Am J Food Technol 2(7):582–592

    Article  Google Scholar 

  • Chinchole M, Pathak RK, Singh UM, Kumar A (2017) Molecular characterization of EcCIPK24 gene of finger millet (Eleusine coracana) for investigating its regulatory role in calcium transport. 3 Biotech 7(4):267

    Article  Google Scholar 

  • Conesa A, Gotz S (2008) Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008:619832. https://doi.org/10.1155/2008/619832

    Article  CAS  PubMed  Google Scholar 

  • Derbyshire MK, Gonzales NR, Lu S, He J, Marchler GH, Wang Z, Marchler-Bauer A (2015) Improving the consistency of domain annotation within the Conserved Domain Database. Database (Oxford). 12;2015. pii: bav012. https://doi.org/10.1093/database/bav012

  • Devi PB, Vijayabharathi R, Sathyabama S, Malleshi NG, Priyadarisini VB (2014) Health benefits of finger millet (Eleusine coracana L.) polyphenols and dietary fiber: a review. J Food Sci Technol 51:1021–1040

    Article  CAS  Google Scholar 

  • Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38(Web Server issue):W64–W70. https://doi.org/10.1093/nar/gkq310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • FAOSTAT (2004) Food and agriculture organization statistical database. http://www.fao.org/docrep/T0818E/T0818E05.htm

  • Garg VK, Avashthi H, Tiwari A, Jain PA, Ramkete PW, Kayastha AM, Singh VK (2016) MFPPI -Multi FASTA ProtParam interface. Bioinformation 12:74–77

    Article  Google Scholar 

  • Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: John MW (ed) The proteomics protocols handbook. Humana Press, New York, pp. 571–607

    Chapter  Google Scholar 

  • Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48:909–930

    Article  CAS  Google Scholar 

  • Gill SS, Khan NA, Anjum NA, Tuteja N (2011) Amelioration of cadmium stress in crop plants by nutrients management: morphological, physiological and biochemical aspects. In: Anjum NA, Lopez-Lauri F (eds) Plant nutrition and abiotic stress tolerance III, plant stress 5 (Special Issue 1). Global Science Books Ltd., Ikenobe, pp 1–23

    Google Scholar 

  • Gopalan C, Sastri R, Subramaniam B (1999) Nutritive values of Indian food. National Institute of Nutrition, Indian Council of Medical Research, Hyderabad

    Google Scholar 

  • Gopalan C, Ramashastri BV, Balasubramanium SC (2004) Nutritive value of Indian foods. National Institute of Nutrition (NIN), Indian Council of Medical Research, Hyderabad, 59–67

    Google Scholar 

  • Graf E, Eaton JW (1990) Antioxidant functions of phytic acid. Free Radic Biol Med 8:61–69

    Article  CAS  Google Scholar 

  • Gupta S, Pathak RK, Gupta SM, Gaur VS, Singh NK, Kumar A (2018) Identification and molecular characterization of Dof transcription factor gene family preferentially expressed in developing spikes of Eleusine coracana L. 3 Biotech 8(2):82

    Article  Google Scholar 

  • Guruprasad K, Reddy BV, Pandit MW (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Prot Eng 4:155–164

    Article  CAS  Google Scholar 

  • Halliwell B (2006) Reactive species and antioxidants. Redox biology is a fundamental theme of aerobic life. Plant Physiol 141:312–322

    Article  CAS  Google Scholar 

  • Ignacimuthu S, Ceasar SA (2012) Development of transgenic finger millet (Eleusine coracana (L.) Gaertn.) resistant to leaf blast disease. J Biosci 37:135–147

    Article  CAS  Google Scholar 

  • Ikai AJ (1980) Thermostability and aliphatic index of globular proteins. J Biochem 88:1895–1898

    CAS  PubMed  Google Scholar 

  • Kaur C, Kapoor HC (2001) Antioxidants in fruits and vegetables-The millennium’s health. Int J Food Sci Technol 36:703–725

    Article  CAS  Google Scholar 

  • Kokane SB, Pathak RK, Singh M, Kumar A (2018) The role of tripartite interaction of calcium sensors and transporters in the accumulation of calcium in finger millet grain. Biologia Plantarum 62(2):325–334

    Article  CAS  Google Scholar 

  • Kumar A, Mirza N, Charan T, Sharma N, Gaur VS (2014) Isolation, characterization and immunolocalization of a seed dominant Cam from finger millet (Eleusine coracana L. Gartn.) for studying its functional role in differential accumulation of calcium in developing grains. Appl Biochem Biotechnol 172:2955–2973

    Article  CAS  Google Scholar 

  • Kumar A, Gaur VS, Goel A, Gupta AK (2015a) De Novo Assembly and Characterization of Developing Spikes Transcriptome of Finger Millet (Eleusine coracana): a Minor Crop Having Nutraceutical Properties. 33:905–922

  • Kumar A, Pathak RK, Gupta SM, Gaur VS, Pandey D (2015b) Systems biology for smart crops and agricultural innovation: filling the gaps between genotype and phenotype for complex traits linked with robust agricultural productivity and sustainability. Omics: J Integr Biol 19:581–601

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016a) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

    Article  CAS  PubMed  Google Scholar 

  • Kumar A, Metwal M, Kaur S, Gupta AK, Puranik S, Singh S, Singh M, Gupta S, Babu BK, Sood S, Yadav R (2016b) Nutraceutical value of finger millet [Eleusine coracana (L.) Gaertn.], and their improvement using omics approaches. Front Plant Science 7:934

    Google Scholar 

  • Kumari L, Sumathi S (2002) Effect of consumption of finger millet on hyperglycemia in non-insulin dependent diabetes mellitus (NIDDM) subjects. Plant Foods Hum Nutr 57:205–213

    Article  Google Scholar 

  • Lobo V, Patil A, Phatak A, Chandra N (2010) Free radicals, antioxidants and functional foods: Impact on human health. Pharmacogn Rev 4:118–126

    Article  CAS  Google Scholar 

  • Maheshwari R, Dubey RS (2009) Nickel-induced oxidative stress and the role of antioxidant defense in rice seedlings. Plant Growth Regul 59:37–49

    Article  CAS  Google Scholar 

  • Meriga B, Reddy BK, Rao KR, Reddy LA, Kishor PBK (2004) Aluminium-induced production of oxygen radicals, lipid peroxidation and DNA damage in seedlings of rice (Oryza sativa). J Plant Physiol 161:63–68

    Article  CAS  Google Scholar 

  • Miller G, Suzuki N, Ciftci-Yilmaz S, Mittler R (2010) Reactive oxygen species homeostasis and signalling during drought and salinity stresses. Plant Cell Environ 33:453–467

    Article  CAS  Google Scholar 

  • Mishra S, Jha AB, Dubey RS (2011) Arsenite treatment induces oxidative stress, upregulates antioxidant system, and causes phytochelatin synthesis in rice seedlings. Protoplasma 248:565–577

    Article  CAS  Google Scholar 

  • Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405–410

    Article  CAS  Google Scholar 

  • Nath M, Goel A, Taj G, Kumar A (2010) Molecular cloning and comparative in silico analysis of calmodulin genes from cereals and millets for understanding the mechanism of differential calcium accumulation. J Proteom Bioinforma 3:294–301

    CAS  Google Scholar 

  • Noctor G, Foyer CH (1998) Ascorbate and glutathione: keeping active oxygen under control. Annu Rev Plant Biol 49:249–279

    Article  CAS  Google Scholar 

  • Obilana AB, Manyasa E (2002) “Millets”. In: Belton PS, Taylor JRN (eds) Pseudocereals and Less Common Cereals. Grain Properties and Utilization Potential. Springer-Verlag, Berlin, pp 176–217

    Google Scholar 

  • Panwar P, Nath M, Yadav VK, Kumar A (2010) Comparative evaluation of genetic diversity using RAPD, SSR and cytochome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.). J Genet 89:121–133

    Article  CAS  Google Scholar 

  • Pathak RK, Baunthiyal M, Shukla R, Pandey D, Taj G, Kumar A (2017) In silico identification of mimicking molecules as defense inducers triggering jasmonic acid mediated immunity against Alternaria blight disease in Brassica species. Front Plant Sci 8:609. https://doi.org/10.3389/fpls.2017.00609

    Article  PubMed  PubMed Central  Google Scholar 

  • Rahman K (2007) Studies on free radicals, antioxidants, and co-factors. Clin Interv Aging 2:218–238

    Google Scholar 

  • Rajasekaran NS, Nithya M, Rose C, Chandra TS (2004) The effect of finger millet feeding on the early responses during the process of wound healing in diabetic rats. Biochimica Biophysica Acta 1689:190–201

    Article  CAS  Google Scholar 

  • Scalbert A, Manach C, Morand C, Remesy C (2005) Dietary polyphenols and prevention of diseases. Crit Rev Food Sci Nutr 45:287–306. https://doi.org/10.1080/1040869059096

    Article  CAS  PubMed  Google Scholar 

  • Seetharam A, Riley KW, Harinarayana G (1986) Small millets in global agriculture. In: Proceedings of the First International Small Millets Workshop, Oct 29–Nov 2, 1986, Bangalore, India, 21–23

  • Shah K, Kumar RG, Verma S, Dubey RS (2001) Effect of cadmium on lipid peroxidation, superoxide anion generation and activities of antioxidant enzymes in growing rice seedlings. Plant Sci 161:1135–1144

    Article  CAS  Google Scholar 

  • Shahidi F, Chandrasekara A (2013) Millet grain phenolics and their role in disease risk reduction and health promotion: a review. J Funct Foods 5:570–581

    Article  CAS  Google Scholar 

  • Sharma P, Dubey RS (2005) Drought induces oxidative stress and enhances the activities of antioxidant enzymes in growing rice seedlings. Plant Growth Regul 46:209–221

    Article  CAS  Google Scholar 

  • Sharma P, Jha AB, Dubey RS, Pessarakli M (2012) Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. J Bot. https://doi.org/10.1155/2012/217037

    Article  Google Scholar 

  • Singh UM, Chandra M, Shankhdhar SC, Kumar A (2014) Transcriptome wide identification and validation of calcium sensor gene family in the developing spikes of finger millet genotypes for elucidating its role in grain calcium accumulation. PLoS One 26 9(8):e103963. https://doi.org/10.1371/journal.pone.0103963

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sripriya G, Chandrasekharan K, Murty VS, Chandra TS (1996) ESR spectroscopic studies on free radical quenching action of finger millet (Eleusine coracana). Food Chem 57:537–540

    Article  CAS  Google Scholar 

  • Srivastava S, Dubey RS (2011) Manganese-excess induces oxidative stress, lowers the pool of antioxidants and elevates activities of key antioxidative enzymes in rice seedlings. Plant Growth Regul 64:1–16

    Article  CAS  Google Scholar 

  • Tiwari A, Avashthi H, Jha R, Srivastava A, Garg VK, Ramteke PW, Kumar A (2016) Insights using the molecular model of Lipoxygenase from Finger millet (Eleusine coracana (L.)). Bioinformation 12:156–164

    Article  Google Scholar 

  • Tsao R (2010) Chemistry and biochemistry of dietary polyphenols. Nutrients 2:1231–1246. https://doi.org/10.3390/nu2121231

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Verma S, Dubey RS (2003) Lead toxicity induces lipid peroxidation and alters the activities of antioxidant enzymes in growing rice plants. Plant Sci 164:645–655

    Article  CAS  Google Scholar 

  • Zhang F, Wan X, Zheng Y, Sun L, Chen Q, Zhu X, Guo Y, Liu M (2013) Effects of nitrogen on the activity of antioxidant enzymes and gene expression in leaves of Populus plants subjected to cadmium stress. J Plant Interact 9:599–609

    Article  Google Scholar 

  • Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinf 14;12 Suppl 14:S2. https://doi.org/10.1186/1471-2105-12-S14-S2

    Article  CAS  Google Scholar 

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Acknowledgements

We gratefully acknowledge the Bioinformatics Centre (Sub DIC) at G. B. Pant University of Agriculture and Technology, Pantnagar, Udham Singh Nagar, Uttarakhand, India and Bioinformatics Centre (DIC) at ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India for providing research facilities.

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Author notes

  1. Rajesh Kumar Pathak

    Present address: School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India

  2. Anil Kumar

    Present address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India

Authors and Affiliations

  1. Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India

    Himanshu Avashthi

  2. Agricultural Knowledge Management Unit, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India

    Himanshu Avashthi & Amrendra Kumar Mishra

  3. Department of Biotechnology, Govind Ballabh Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand, India

    Rajesh Kumar Pathak

  4. Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi, India

    Neetesh Pandey

  5. Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India

    Sandeep Arora & Anil Kumar

  6. Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia

    Vijai Kumar Gupta

  7. Department of Biological Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India

    Pramod Wasudeo Ramteke

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  1. Himanshu Avashthi
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Contributions

PWR and AK conceptualized the idea of manuscript and supervised all the experiments. HA performed all the experiments interpreted the results and formulated the manuscript independently. NP helped in Gene Ontology analysis. RKP and AKM assisted, edited, and updated the manuscript. RKP, SA, AKM, VKG, PWR, and AK contributed critically by revising the draft, provided valuable suggestions, and updating the manuscript for publication.

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Correspondence to Himanshu Avashthi, Pramod Wasudeo Ramteke or Anil Kumar.

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Avashthi, H., Pathak, R.K., Pandey, N. et al. Transcriptome-wide identification of genes involved in Ascorbate–Glutathione cycle (Halliwell–Asada pathway) and related pathway for elucidating its role in antioxidative potential in finger millet (Eleusine coracana (L.)). 3 Biotech 8, 499 (2018). https://doi.org/10.1007/s13205-018-1511-9

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