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Identification and characterization of RNA polymerase II (RNAP) C-Terminal domain phosphatase-like 3 (SlCPL3) in tomato under biotic stress

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Abstract

Background

Bacterial diseases are a huge threat to the production of tomatoes. During infection intervals, pathogens affect biochemical, oxidant and molecular properties of tomato. Therefore, it is necessary to study the antioxidant enzymes, oxidation state and genes involved during bacterial infection in tomato.

Methods and results

Different bioinformatic analyses were performed to conduct homology, gene promoter analysis and determined protein structure. Antioxidant, MDA and H2O2 response was measured in Falcon, Rio grande and Sazlica tomato cultivars. In this study, RNA Polymerase II (RNAP) C-Terminal Domain Phosphatase-like 3 (SlCPL-3) gene was identified and characterized. It contained 11 exons, and encoded for two protein domains i.e., CPDCs and BRCT. SOPMA and Phyre2, online bioinformatic tools were used to predict secondary structure. For the identification of protein pockets CASTp web-based tool was used. Netphos and Pondr was used for prediction of phosphorylation sites and protein disordered regions. Promoter analysis revealed that the SlCPL-3 is involved in defense-related mechanisms. We further amplified two different regions of SlCPL-3 and sequenced them. It showed homology respective to the reference tomato genome. Our results showed that SlCPL-3 gene was triggered during bacterial stress. SlCPL-3 expression was upregulated in response to bacterial stress during different time intervals. Rio grande showed a high level of SICPL-3 gene expression after 72 hpi. Biochemical and gene expression analysis showed that under biotic stress Rio grande cultivar is more sensitive to Pst DC 3000 bacteria.

Conclusion

This study lays a solid foundation for the functional characterization of SlCPL-3 gene in tomato cultivars. All these findings would be beneficial for further analysis of SlCPL-3 gene and may be helpful for the development of resilient tomato cultivars.

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Data Availability

The data will be made available on reasonable request to corresponding author.

Abbreviations

PCR:

Polymerase Chain Reaction

LB media:

Lysogeny Broth media

BRCT:

Breast Cancer C Terminus

CPDC:

Catalytic domain of C- terminal domain-like phosphatases

CDKCs:

Cyclin dependent kinases

Hpi:

Hours post infiltration

H2O2 :

Hydrogen peroxide

Bp:

Base pair

References

  1. Balmant KM, Parker J, Yoo MJ et al (2015) Redox proteomics of tomato in response to Pseudomonas syringae infection. Hortic Res. https://doi.org/10.1038/hortres.2015.43. 2:

    Article  PubMed  PubMed Central  Google Scholar 

  2. Quinet M, Angosto T, Yuste-Lisbona FJ et al (2019) Tomato Fruit Development and Metabolism. Front. Plant Sci. 10

  3. Anzalone A, Mosca A, Dimaria G et al (2022) Soil and Soilless Tomato Cultivation promote different microbial Communities that provide New Models for Future Crop Interventions. Int J Mol Sci 23. https://doi.org/10.3390/ijms23158820

  4. Arslan Ş, Arısoy H, Karakayacı Z (2022) The Situation of Regional Concentration of Tomato Foreign Trade in Turkey. Turkish J Agric - Food Sci Technol 10:280–289. https://doi.org/10.24925/turjaf.v10i2.280-289.4767

    Article  Google Scholar 

  5. Li Y, Wang H, Zhang Y, Martin C (2018) Can the world’s favorite fruit, tomato, provide an effective biosynthetic chassis for high-value metabolites? Plant Cell Rep 37:1443–1450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Zhao J, Sauvage C, Zhao J et al (2019) Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor. Nat Commun 10. https://doi.org/10.1038/s41467-019-09462-w

  7. Cerda R, Avelino J, Gary C et al (2017) Primary and secondary yield losses caused by pests and diseases: Assessment and modeling in coffee. PLoS ONE 12. https://doi.org/10.1371/journal.pone.0169133

  8. Buttimer C, McAuliffe O, Ross RP et al (2017) Bacteriophages and bacterial plant diseases. Front Microbiol 8

  9. Thomas NC, Hendrich CG, Gill US et al (2020) The Immune receptor Roq1 confers resistance to the bacterial pathogens Xanthomonas, Pseudomonas syringae, and Ralstonia in Tomato. Front Plant Sci 11. https://doi.org/10.3389/fpls.2020.00463

  10. Hamdoun S, Liu Z, Gill M et al (2013) Dynamics of defense responses and cell fate change during Arabidopsis-Pseudomonas syringae interactions. PLoS ONE 8. https://doi.org/10.1371/journal.pone.0083219

  11. Chassot C, Nawrath C, Métraux JP (2007) Cuticular defects lead to full immunity to a major plant pathogen. Plant J 49:972–980. https://doi.org/10.1111/j.1365-313X.2006.03017.x

    Article  CAS  PubMed  Google Scholar 

  12. Lewis LA, Polanski K, de Torres-Zabala M et al (2015) Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv tomato DC3000. Plant Cell 27:3038–3064. https://doi.org/10.1105/tpc.15.00471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Derksen H, Rampitsch C, Daayf F (2013) Signaling cross-talk in plant disease resistance. Plant Sci 207:79–87

    Article  CAS  PubMed  Google Scholar 

  14. Bowler C, Fluhr R (2000) The role of calcium and activated oxygens as signals for controlling cross-tolerance. Trends Plant Sci 5:241–246. https://doi.org/10.1016/S1360-1385(00)01628-9

    Article  CAS  PubMed  Google Scholar 

  15. Lamb C, Dixon RA (1997) The oxidative burst in plant disease resistance. Annu Rev Plant Biol 48:251–275. https://doi.org/10.1146/annurev.arplant.48.1.251

    Article  CAS  Google Scholar 

  16. Passardi F, Cosio C, Penel C, Dunand C (2005) Peroxidases have more functions than a swiss army knife. Plant Cell Rep 24:255–265

    Article  CAS  PubMed  Google Scholar 

  17. Watanabe S, Sato M, Sawada Y et al (2018) Arabidopsis molybdenum cofactor sulfurase ABA3 contributes to anthocyanin accumulation and oxidative stress tolerance in ABA-dependent and independent ways. Sci Rep 8. https://doi.org/10.1038/s41598-018-34862-1

  18. Blokhina O, Virolainen E, Fagerstedt KV (2003) Antioxidants, oxidative damage and oxygen deprivation stress: a review. Ann Bot 91:179–194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Nowogórska A, Patykowski J (2015) Selected reactive oxygen species and antioxidant enzymes in common bean after Pseudomonas syringae pv. Phaseolicola and Botrytis cinerea infection. Acta Physiol Plant 37. https://doi.org/10.1007/s11738-014-1725-3

  20. Qiu JL, Zhou L, Yun BW et al (2008) Arabidopsis mitogen-activated protein kinase kinases MKK1 and MKK2 have overlapping functions in defense signaling mediated by MEKK1, MPK4, and MKS1. Plant Physiol 148:212–222. https://doi.org/10.1104/pp.108.120006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. AbuQamar S, Chai MF, Luo H et al (2008) Tomato protein kinase 1b mediates signaling of plant responses to necrotrophic fungi and insect herbivory. Plant Cell 20:1964–1983. https://doi.org/10.1105/tpc.108.059477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Hirose Y, Manley JL (2000) RNA polymerase II and the integration of nuclear events. Genes Dev 14:1415–1429. https://doi.org/10.1101/GAD.14.12.1415

    Article  CAS  PubMed  Google Scholar 

  23. Koiwa H, Barb AW, Xiong L et al (2002) C-terminal domain phosphatase-like family members (AtCPLs) differentially regulate Arabidopsis thaliana abiotic stress signaling, growth, and development. Proc Natl Acad Sci U S A 99:10893–10898. https://doi.org/10.1073/pnas.112276199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Koiwa H, Bressan RA, Hasegawa PM (2006) Identification of plant stress-responsive determinants in arabidopsis by large-scale forward genetic screens. In: Journal of Experimental Botany. pp 1119–1128

  25. Koiwa H, Hausmann S, Bang WY et al (2004) Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases. Proc Natl Acad Sci U S A 101:14539–14544. https://doi.org/10.1073/pnas.0403174101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Koiwa H (2006) Phosphorylation of RNA polymerase II C-terminal domain and plant osmotic-stress responses. In: Abiotic Stress Tolerance in Plants. Springer Netherlands, pp 47–57

  27. Li F, Cheng C, Cui F et al (2014) Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity. Cell Host Microbe 16:748–758. https://doi.org/10.1016/j.chom.2014.10.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Geourjon C, Deléage G (1995) Sopma: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics 11:681–684. https://doi.org/10.1093/bioinformatics/11.6.681

    Article  CAS  Google Scholar 

  29. Kelley LA, Mezulis S, Yates CM et al (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845–858. https://doi.org/10.1038/nprot.2015.053

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Tian W, Chen C, Lei X et al (2018) CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res 46:W363–W367. https://doi.org/10.1093/nar/gky473

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Li X, Sun Z, Shao S et al (2015) Tomato-Pseudomonas syringae interactions under elevated CO2 concentration: the role of stomata. J Exp Bot 66:307–316. https://doi.org/10.1093/jxb/eru420

    Article  CAS  PubMed  Google Scholar 

  32. MARKLUND S, MARKLUND G (1974) Involvement of the Superoxide Anion Radical in the autoxidation of Pyrogallol and a convenient assay for Superoxide dismutase. Eur J Biochem 47:469–474. https://doi.org/10.1111/j.1432-1033.1974.tb03714.x

    Article  CAS  PubMed  Google Scholar 

  33. Diao M, Ma L, Wang J et al (2014) Selenium promotes the growth and photosynthesis of Tomato Seedlings under Salt stress by enhancing chloroplast antioxidant Defense System. J Plant Growth Regul 33:671–682. https://doi.org/10.1007/s00344-014-9416-2

    Article  CAS  Google Scholar 

  34. Bustin SA, Benes V, Garson JA et al (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55:611–622. https://doi.org/10.1373/clinchem.2008.112797

    Article  CAS  PubMed  Google Scholar 

  35. Yuan JS, Reed A, Chen F, Stewart CN (2006) Statistical analysis of real-time PCR data. BMC Bioinformatics 7. https://doi.org/10.1186/1471-2105-7-85

  36. Stank A, Kokh DB, Fuller JC, Wade RC (2016) Protein binding Pocket Dynamics. Acc Chem Res 49:809–815. https://doi.org/10.1021/acs.accounts.5b00516

    Article  CAS  PubMed  Google Scholar 

  37. Bang W, Kim S, Ueda A et al (2006) Arabidopsis carboxyl-terminal domain phosphatase-like isoforms share common catalytic and interaction domains but have distinct in planta functions. Plant Physiol 142:586–594. https://doi.org/10.1104/pp.106.084939

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Hussain A, Yun BW, Kim JH et al (2019) Novel and conserved functions of S-nitrosoglutathione reductase in tomato. J Exp Bot 70:4877–4886. https://doi.org/10.1093/JXB/ERZ234

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ray S, Mondal S, Chowdhury S, Kundu S (2015) Differential responses of resistant and susceptible tomato varieties to inoculation with Alternaria solani. Physiol Mol Plant Pathol 90:78–88. https://doi.org/10.1016/j.pmpp.2015.04.002

    Article  CAS  Google Scholar 

  40. Muday GK, Brown-Harding H (2018) Nervous system-like signaling in plant defense herbivory induces rapid long-distance calcium signals through glutamate-l ike receptors. Science 361:1068–1069 (80-.)

    Article  CAS  PubMed  Google Scholar 

  41. Taverne YJ, Merkus D, Bogers AJ et al (2018) Reactive oxygen species: radical factors in the evolution of Animal Life: a molecular timescale from Earth’s earliest history to the rise of complex life. https://doi.org/10.1002/bies.201700158. BioEssays 40:

  42. Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55:373–399

    Article  CAS  PubMed  Google Scholar 

  43. Lobna H, Aymen EM, Hajer R et al (2017) Biochemical and plant nutrient alterations induced by Meloidogyne javanica and Fusarium oxysporum f.Sp.radicis lycopersici co-infection on tomato cultivars with differing level of resistance to M. javanica. Eur J Plant Pathol 148:463–472. https://doi.org/10.1007/s10658-016-1104-6

    Article  CAS  Google Scholar 

  44. Vanderspool MC, Kaplan DT, McCollum TG, Wodzinski RJ (1994) Partial characterization of cytosolic superoxide dismutase activity in the interaction of Meloidogyne incognita with two cultivars of Glycine max. J Nematol 26:422–429

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Zacheo G, Bleve-Zacheo T (1988) Involvement of superoxide dismutases and superoxide radicals in the susceptibility and resistance of tomato plants to Meloidogyne incognita attack. Physiol Mol Plant Pathol 32:313–322. https://doi.org/10.1016/S0885-5765(88)80026-2

    Article  CAS  Google Scholar 

  46. Debona D, Rodrigues F, Rios JA, Nascimento KJT (2012) Biochemical changes in the leaves of wheat plants infected by Pyricularia oryzae. Phytopathology 102:1121–1129. https://doi.org/10.1094/PHYTO-06-12-0125-R

    Article  CAS  PubMed  Google Scholar 

  47. Shu P, Zhang S, Li Y et al Over-expression of SlWRKY46 in tomato plants increases susceptibility to Botrytis cinerea by modulating ROS homeostasis and SA and JA signaling. Elsevier

  48. Yao N, Greenberg JT (2006) Arabidopsis ACCELERATED CELL DEATH2 modulates programmed cell death. Plant Cell 18:397–411. https://doi.org/10.1105/tpc.105.036251

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Meena M, Zehra A, Dubey MK et al (2016) Comparative evaluation of biochemical changes in tomato (Lycopersicon esculentum Mill.) Infected by alternaria alternata and its toxic metabolites (TeA, AOH, and AME). Front Plant Sci 7. https://doi.org/10.3389/fpls.2016.01408

  50. Gadjev I, Stone JM, Gechev TS (2008) Chap. 3: programmed cell death in plants. New Insights into Redox Regulation and the role of Hydrogen Peroxide. Int Rev Cell Mol Biol 270:87–144

    Article  CAS  PubMed  Google Scholar 

  51. Tran BQ, Jung S (2020) Modulation of chloroplast components and defense responses during programmed cell death in tobacco infected with Pseudomonas syringae. Biochem Biophys Res Commun 528:753–759. https://doi.org/10.1016/j.bbrc.2020.05.086

    Article  CAS  PubMed  Google Scholar 

  52. Silva LC, Debona D, Aucique-Pérez CE et al (2020) Physiological and antioxidant insights into common bean resistance to common bacterial blight. Physiol Mol Plant Pathol 111. https://doi.org/10.1016/j.pmpp.2020.101505

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Acknowledgements

This study is part of the Ph.D. thesis work of Faisal Saeed who is doctoral candidate working under the supervision of Ufuk Demirel and Allah Bakhsh. The authors acknowledge the Ayhan Şahenk Foundation for providing fellowship during the doctoral study of FS. Authors are also grateful to Dr. Eminur Elçi, Associate Professor, Department of Plant Production and Technologies, Nigde Omer Halisdemir University for providing seeds of tomato cultivars.

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Authors and Affiliations

  1. Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey

    Faisal Saeed, Muneeb Hassan Hashmi, Ufuk Demirel & Allah Bakhsh

  2. Dept. of Biological Sciences, Middle East Technical University, 06800, Cankaya, Ankara, Turkey

    Emre Aksoy

  3. Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan

    Allah Bakhsh

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  1. Faisal Saeed
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  2. Muneeb Hassan Hashmi
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Contributions

EA, AB and FS conceived the idea. FS performed the experiments, collected data and wrote the initial draft of manuscript. AB, EA and UD corrected the manuscript. MHH helped data interpretation. UD and AB supervised the overall study, and all authors approved the final draft.

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Correspondence to Allah Bakhsh.

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Saeed, F., Hashmi, M.H., Aksoy, E. et al. Identification and characterization of RNA polymerase II (RNAP) C-Terminal domain phosphatase-like 3 (SlCPL3) in tomato under biotic stress. Mol Biol Rep 50, 6783–6793 (2023). https://doi.org/10.1007/s11033-023-08564-5

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