Molecular Biology Reports

, Volume 41, Issue 3, pp 1385–1399 | Cite as

Differential gene expression profile in Pseudomonas putida NBRIC19-treated wheat (Triticum aestivum) plants subjected to biotic stress of Parthenium hysterophorus

  • Sandhya Mishra
  • Suchi Srivastava
  • Chandra Shekhar Nautiyal


The inoculation of Pseudomonas putida NBRIC19 protected wheat plant from phytotoxic effect of Parthenium hysterophorus (Parthenium) and enhanced root length, shoot length, dry weight, spike length and chlorophyll content. With the aim to screen for genes differentially expressed in P. putida NBRIC19-inoculated wheat grown along with Parthenium (WPT), the suppression subtractive hybridization (SSH) methodology was employed. The SSH analysis was performed with WPC (uninoculated wheat grown along with Parthenium) as driver and WPT as tester. The cDNA library, enriched with differentially expressed ESTs (expressed sequence tags), were constructed from WPT. Following an initial screen of 165 ESTs in our library, 32 ESTs were identified, annotated and further validated by semiquantitative RT-PCR. The differentially expressed ESTs were associated with general stress response, defense response, growth and development, metabolic process, photosynthesis, signal transduction, and some other with unknown function. Five ESTs showing downregulation in expression level in response to Parthenium got upregulated due to P. putida NBRIC19 inoculation and further validated by quantitative real time PCR analysis at different time intervals viz. 15, 30, 45 and 90 days. SSH has been implemented for the first time to gain insights into molecular events underlying successful role of P. putida NBRIC19 in providing protection to wheat against Parthenium. The information generated in this study provides new clues to aid the understanding of genes corresponding to differentially expressed ESTs putatively involved in allelopathic interactions. Further characterization and functional analysis of these genes may provide valuable information for future studies of the molecular mechanism by which plants adapt to allelopathic effect of Parthenium.


Parthenium Suppression subtractive hybridization Pseudomonas putida Wheat Gene expression Real time PCR 



The study was supported by Task Force Grant NWP-006 from Council of Scientific and Industrial Research (CSIR), New Delhi, India. Part of the work was supported by TATA Innovation Fellowship awarded to Dr. Chandra Shekhar Nautiyal by Department of Biotechnology, Government of India. Sandhya Mishra would like to thank CSIR for awarding Senior Research Fellowship.


  1. 1.
    Cao Y, Wu Y, Zheng Z, Song F (2006) Overexpression of the rice EREBP-like gene OsBIERF3 enhances disease resistance and salt tolerance in transgenic tobacco. Physiol Mol Plant Pathol 67:202–211CrossRefGoogle Scholar
  2. 2.
    Orellana S, Yanez M, Espinoza A, Verdugo I, Gonzalez E, Ruiz-Lara S, Casaretto JA (2010) The transcription factor SlAREB1 confers drought, salt stress tolerance and regulates biotic and abiotic stress-related genes in tomato. Plant Cell Environ 33:2191–2208PubMedCrossRefGoogle Scholar
  3. 3.
    Fässler E, Plaza S, Pairraud A, Gupta SK, Robinson B, Schulina R (2011) Expression of selected genes involved in cadmium detoxification in tobacco plants grown on a sulphur-amended metal-contaminated field. Environ Exp Bot 70:158–165CrossRefGoogle Scholar
  4. 4.
    Way H, Chapman S, McIntyre L, Casu R, Xue GP, Manners J, Shorter R (2005) Identification of differentially expressed genes in wheat undergoing gradual water deficit stress using a subtractive hybridisation approach. Plant Sci 168:661–670CrossRefGoogle Scholar
  5. 5.
    Saranga Y, Paterson AH, Levi A (2009) Bridging classical and molecular genetics of abiotic stress resistance in cotton. Plant Genet Genomics: Crops Model 3:1–16Google Scholar
  6. 6.
    Liu F, Xu W, Wei Q, Zhang Z, Xing Z, Tan L, Di C, Yao D, Wang C, Tan Y, Yan H, Ling Y, Sun C, Xue Y, Su Z (2010) Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica) and 93-11 (Indica) during oxidative stress. PLoS ONE 5:e8632PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Taji T, Seki M, Satou M, Sakurai T, Kobayashi M, Ishiyama K, Narusaka Y, Narusaka M, Zhu JK, Shinozaki K (2004) Comparative genomics in salt tolerance between Arabidopsis and Arabidopsis-related halophyte salt stress using Arabidopsis microarray. Plant Physiol 135:1697–1709PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Fujita Y, Fujita M, Satoh R, Maruyama K, Parvez MM, Seki M, Hiratsu K, Ohme-Takagi M, Shinozaki K, Yamaguchi-Shinozaki K (2005) AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell 17:3470–3488PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Blanco FA, Zanetti ME, Casalongué CA, Daleo GR (2006) Molecular characterization of a potato MAP kinase transcriptionally regulated by multiple environmental stresses. Plant Physiol Biochem 44:315–322PubMedCrossRefGoogle Scholar
  10. 10.
    Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803PubMedCrossRefGoogle Scholar
  11. 11.
    Gao JP, Chao DY, Lin HX (2007) Understanding abiotic stress tolerance mechanisms: recent studies on stress response in rice. J Integr Plant Biol 49:742–750CrossRefGoogle Scholar
  12. 12.
    Shulaev V, Cortes D, Miller G, Mittler R (2009) Metabolomics for plant stress response. Physiol Plant 132:199–208CrossRefGoogle Scholar
  13. 13.
    Latch GCM (1993) Physiological interactions of endophytic fungi and their hosts. Biotic stress tolerance imparted to grasses by endophytes. Agric Ecosyst Environ 44:143–156CrossRefGoogle Scholar
  14. 14.
    Timmusk S, Wagner EGH (1999) The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol Plant Micro Int 12:951–959CrossRefGoogle Scholar
  15. 15.
    Alfano G, Ivey MLL, Cakir C, Bos JIB, Miller SA, Madden LV, Kamoun S, Hoitink HAJ (2007) Systemic modulation of gene expression in tomato by Trichoderma hamatum 382. Phytopathol 97:429–437CrossRefGoogle Scholar
  16. 16.
    Van Loon L (2007) Plant responses to plant growth promoting rhizobacteria. Eur J Plant Pathol 119:243–254CrossRefGoogle Scholar
  17. 17.
    Dardanelli MS, Manyani H, González-Barroso S, Rodríguez-Carvajal MA, Gil-Serrano AM, Espuny MR, López-Baena FJ, Bellogín RA, Megías M, Ollero FJ (2010) Effect of the presence of the plant growth promoting rhizobacterium (PGPR) Chryseobacterium balustinum Aur9 and salt stress in the pattern of flavonoids exuded by soybean roots. Plant Soil 328:483–493CrossRefGoogle Scholar
  18. 18.
    Radosevich SR (1987) Methods to study interactions among crops and weeds. Weed Technol 1:190Google Scholar
  19. 19.
    Evans HC (1997) Parthenium hysterophorus: a review of its weed status and the possibilities for biological control. Biocontrol News Inform 18:389–398Google Scholar
  20. 20.
    Mersie W, Singh M (1987) Allelopathic effect of Parthenium (Parthenium hysterophorus L.) extract and residue on some agronomic crops and weeds. J Chem Ecol 13:1739–1747PubMedCrossRefGoogle Scholar
  21. 21.
    Mishra S, Nautiyal CS (2012) Reducing the allelopathic effect of Parthenium hysterophorous L. on wheat (Triticum aestivum L.) by Pseudomonas putida. Plant Growth Regul 66:155–165CrossRefGoogle Scholar
  22. 22.
    Mishra S, Mishra A, Chauhan PS, Mishra SK, Kumari M, Niranjan A, Nautiyal CS (2012) Pseudomonas putida NBRIC19 dihydrolipoamide succinyltransferase (SucB) gene controls degradation of toxic allelochemicals produced by Parthenium hysterophorus. J Appl Microbiol 112:793–808PubMedCrossRefGoogle Scholar
  23. 23.
    Mishra S, Chauhan PS, Goel AK, Upadhyay RS, Nautiyal CS (2012) Pseudomonas putida NBRIC19 provides protection to neighboring plant diversity from invasive weed Parthenium hysterophorus L. by altering soil microbial community. Acta Physiol Plant 34:2187–2195CrossRefGoogle Scholar
  24. 24.
    Geng H, Shi L, Li W, Zhang B, Chu C, Li H, Zhang G (2008) Gene expression of jojoba (Simmondsia chinensis) leaves exposed to drying. Environ Exp Bot 63:137–146CrossRefGoogle Scholar
  25. 25.
    Xu J, Belanger F, Huang B (2008) Differential gene expression in shoots and roots under heat stress for a geothermal and non-thermal Agrostis grass species contrasting in heat tolerance. Environ Exp Bot 63:240–247CrossRefGoogle Scholar
  26. 26.
    Nautiyal CS, Govindarajan R, Lavania M, Pushpangadan P (2008) Novel mechanism of modulating natural antioxidants in functional foods: involvement of plant growth promoting rhizobacteria NRRL B-30488. J Agric Food Chem 56:4474–4481PubMedCrossRefGoogle Scholar
  27. 27.
    McCune B, Mefford MJ (2005) Multivariate analysis on the PC-ORD system. Version 5. MjM Software, Gleneden BeachGoogle Scholar
  28. 28.
    Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14:1–4PubMedCrossRefGoogle Scholar
  29. 29.
    Duressa D, Soliman K, Chen D (2010) Identification of aluminum responsive genes in Al-tolerant soybean line PI 416937. Int J Plant Genomics 2010:1–13Google Scholar
  30. 30.
    Sanghera GS, Wani SH, Hussain W, Singh NB (2011) Engineering cold stress tolerance in crop plants. Curr Genomics 12:30–43PubMedCrossRefGoogle Scholar
  31. 31.
    Hajduch M, Rakwal R, Agrawal GK, Yonekura M, Pretova A (2001) High-resolution two-dimensional electrophoresis separation of proteins from metal stressed rice (Oryza sativa L) leaves: drastic reductions/fragmentations of ribulose-1,5-bisphosphate carboxylase/oxygenase and induction of stress-related proteins. Electrophoresis 22:2824–2831PubMedCrossRefGoogle Scholar
  32. 32.
    Agrawal GK, Jwa NS, Han KS, Agrawal VP, Rakwal R (2003) Isolation of a novel rice PR4 type gene whose mRNA expression is modulated by blast pathogen attack and signaling components. Plant Physiol Biochem 41:81–90CrossRefGoogle Scholar
  33. 33.
    Dunn MA, White AJ, Vural S, Hughes MA (1998) Identification of promoter elements in a low-temperature-responsive gene (blt49) from barley (Hordeum vulgare L). Plant Mol Biol 38:551–564PubMedCrossRefGoogle Scholar
  34. 34.
    Maldonado AM, Doerner P, Dixonk RA, Lamb CJ, Cameron RK (2002) A putative lipid transfer protein involved in systemic resistance signalling in Arabidopsis. Nature 419:399–403PubMedCrossRefGoogle Scholar
  35. 35.
    Carvalho AO, Gomes VM (2007) Role of plant lipid transfer proteins in plant cell physiology: a concise review. Peptides 28:1144–1153CrossRefGoogle Scholar
  36. 36.
    George S, Parida A (2010) Characterization of an oxidative stress inducible nonspecific lipid transfer protein coding cDNA and its promoter from drought tolerant plant Prosopsis juliflora. Plant Mol Biol Rep 28:32–40CrossRefGoogle Scholar
  37. 37.
    Hoshida H, Tanaka Y, Hibino T, Hayashi Y, Tanaka A, Takabe T, Takabe T (2000) Enhanced tolerance to salt stress in transgenic rice that overexpresses chloroplast glutamine synthetase. Plant Mol Biol 43:103–111PubMedCrossRefGoogle Scholar
  38. 38.
    Yang T, Poovaiah BW (2003) Calcium/calmodulin-mediated signal network in plants. Trends Plant Sci 8:505–512PubMedCrossRefGoogle Scholar
  39. 39.
    Holmberg N, Bulow L (1998) Improving stress tolerance in plants by gene transfer. Trends Plant Sci 3:61–66CrossRefGoogle Scholar
  40. 40.
    Giotis ES, McDowell DA, Blair IS, Wilkinson BJ (2007) Role of branched-chain fatty acids in pH stress tolerance in Listeria monocytogenes. Appl Environ Microbiol 73:997–1001PubMedCentralPubMedCrossRefGoogle Scholar
  41. 41.
    Vieira Dos Santos C, Rey P (2006) Plant thioredoxins are key actors in the oxidative stress response. Trends Plant Sci 11:329–334PubMedCrossRefGoogle Scholar
  42. 42.
    Ruelland E, Miginiac-Maslow M (1999) Regulation of chloroplast enzyme activities by thioredoxins: activation or relief from inhibition? Trends Plant Sci 4:136–141PubMedCrossRefGoogle Scholar
  43. 43.
    Broin M, Cuine S, Eymery F, Rey P (2002) The plastidic 2-Cys-peroxiredoxin is a target for a thioredoxin involved in the protection of the photosynthetic apparatus against oxidative damage. Plant Cell 14:1417–1432PubMedCentralPubMedCrossRefGoogle Scholar
  44. 44.
    Broin M, Rey P (2003) Potato plants lacking the CDSP32 plastidic thioredoxin exhibit over-oxidation of the BAS1 2-cys peroxiredoxin and increased lipid peroxidation in thylakoids under photooxidative stress. Plant Physiol 132:1335–1343PubMedCentralPubMedCrossRefGoogle Scholar
  45. 45.
    Witte CP (2011) Urea metabolism in plants. Plant Sci 180:431–438PubMedCrossRefGoogle Scholar
  46. 46.
    Ruan YL, Jin Y, Yang YJ, Li GJ, Boyer JS (2010) Sugar input, metabolism, and signaling mediated by invertase: roles in development, yield potential, and response to drought and heat. Mol Plant 3:942–955PubMedCrossRefGoogle Scholar
  47. 47.
    Li ZM, Palmer WP, Martin AP, Wang RQ, Rainsford F, Jin Y, Patrick JW, Yang YJ, Ruan YL (2012) High invertase activity in tomato reproductive organs correlates with enhanced sucrose import into, and heat tolerance of young fruit. J Exp Bot 63:1155–1166PubMedCrossRefGoogle Scholar
  48. 48.
    Wang L, Ruan YL (2012) New insights into roles of cell wall invertase in early seed development revealed by comprehensive spatial and temporal expression patterns of GhCWIN1 in cotton. Plant Physiol. doi: 10.1104/pp.112.203893 Google Scholar
  49. 49.
    Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He ZH (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374PubMedCrossRefGoogle Scholar
  50. 50.
    Von Schweinichen C, Buttner M (2005) Expression of plant cell wall invertase in roots of Arabidopsis leads to early flowering and an increase in whole plant biomass. Plant Biology 7:469–475CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Sandhya Mishra
    • 1
  • Suchi Srivastava
    • 1
  • Chandra Shekhar Nautiyal
    • 1
  1. 1.Division of Plant Microbe InteractionsCSIR-National Botanical Research InstituteLucknowIndia

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