Abstract
The amino acid, proline, is utilized by different organisms to offset cellular imbalances caused by environmental stresses. The wide use of proline as a stress adaptor molecule indicates that proline has a fundamental biological role in stress response. A comprehensive analysis of the transcript abundance of proline metabolizing genes is fundamental for the assessment of function and regulation of each gene. Using available microarray data and quantitative real-time RT-PCR, the expression profiles of gene encoding key proline biosynthesis and degradation enzymes i.e., OAT, P5CS, P5CR and PDH were examined. Interestingly, validation of candidate genes in rice using in-silico data provided strong evidence for their involvement in stress response. Note that, OsOAT, OsP5CS1, OsP5CS2, OsP5CR showed similar expression pattern in quantitative real-time RT-PCR results as compared to microarray data. However, OsPDH showed a different expression pattern which may be due to the genotypic variation. Furthermore, a biochemical assay measuring proline content gave us a proper indication of the accumulation of proline under stressed conditions. Identification of key proline metabolizing genes from rice and Arabidopsis provides insights on the molecular regulation of proline homeostasis, to initiate metabolic engineering to develop stress-resilient plants.
Similar content being viewed by others
References
Adamipour N, Khosh-Khui M, Salehi H, Razi H, Karami A, Moghadam A (2020) Metabolic and genes expression analyses involved in proline metabolism of two rose species under drought stress. Plant Physiol Biochem 155:105–113. https://doi.org/10.1016/j.plaphy.2020.07.028
Anna J, Sylva Z, Miroslav K, Miroslava V, Ilja TP (2010) Freezing tolerance and proline content of in vitro selected hydroxyproline resistant winter oilseed rape. Czech J Genet Plant Breed 46(1):35–40
Anwar A, Wang K, Wang J et al (2020) Expression of Arabidopsis Ornithine Aminotransferase (AtOAT) encoded gene enhances multiple abiotic stress tolerances in wheat. Plant Cell Rep. https://doi.org/10.1007/s00299-021-02699-0
Armengaud P, Thiery L, Buhot N, March GG, Savoure A (2004) Transcriptional regulation of proline biosynthesis in Medicago truncatula reveals developmental and environmental specific features. Physiol Plant 120(3):442–450. https://doi.org/10.1111/j.0031-9317.2004.00251.x
Bates LS, Waldren RP, Teare ID (1973) Rapid determination of free proline for water-stress studies. Plant Soil 39:205–207. https://doi.org/10.1007/BF00018060
Bhaskara GB, Yang T-H, Verslues PE (2015) Dynamic proline metabolism: importance and regulation in water limited environments. Front Plant Sci 6:484. https://doi.org/10.3389/fpls.2015.00484
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Gallo CT, Bertoni M, Bordoli L, Schwede T (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. https://doi.org/10.1093/nar/gku340
Çelik Ö, Atak C (2011) Evaluation of proline accumulation and Δ1-pyrroline-5-carboxylate Synthetase (P5CS) Gene expression during salinity stress in two soybean (Glycine max L. Merr.) varieties. Pol J Environ Stud 21(3):559–564
Chun SC, Paramasivan M, Chandrasekaran M (2018) Proline accumulation influenced by osmotic stress in arbuscular mycorrhizal symbiotic plants. Front Microbiol 9:2525. https://doi.org/10.3389/fmicb.2018.02525
Deuschle K, Funck D, Forlani G, Stransky H, Biehl A, Leister D, van der Graaff E, Kunze R, Frommera WB (2004) The role of D1-pyrroline-5-carboxylate dehydrogenase in proline degradation. Plant Cell 16(12):3413–3425. https://doi.org/10.1105/tpc.104.023622
Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25):14863–14868. https://doi.org/10.1073/pnas.95.25.14863
Emanuelsson O, Nielsen H, Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8(5):978–984. https://doi.org/10.1110/ps.8.5.978
Fiasconaro ML, Lovato M, Antolín M, Clementi L, Torres N, Gervasio S, Martín C (2019) Role of proline accumulation on fruit quality of pepper (Capsicum annuum L.) grown with a K-rich compost under drought conditions. Sci Hortic 249:280–288. https://doi.org/10.1016/j.scienta.2019.02.002
Funck D, Stadelhofer B, Koch W (2008) Ornithine-δ-aminotransferase is essential for Arginine Catabolism but not for Proline Biosynthesis. BMC Plant Biol 8:40. https://doi.org/10.1186/1471-2229-8-40
Funck D, Eckard S, Müller G (2010) Non- redundant functions of two proline dehydrogenase isoforms in Arabidopsis. BMC Plant Biol 10:70. https://doi.org/10.1186/1471-2229-10-70
Funck D, Winter G, Baumgarten L et al (2012) Requirement of proline synthesis during Arabidopsis reproductive development. BMC Plant Biol 12:191. https://doi.org/10.1186/1471-2229-12-191
Furlan AL, Bianucci E, Giordano W, Castro S, Becker DF (2020) Proline metabolic dynamics and implications in drought tolerance of peanut plants. Plant Physiol Biochem 151:566–578. https://doi.org/10.1016/j.plaphy.2020.04.010
Ginzberg I, Stein H, Kapulnik Y, Szabados L, Strizhov N, Schell J, Koncz C, Zilberstein A (1998) Isolation and characterization of two different DNAs of delta1-pyrroline-5-carboxylate synthase in alfalfa, transcriptionally induced upon salt stress. Plant Mol Biol 38(5):755–764. https://doi.org/10.1023/A:1006015212391
Gupta SC, Sharma A, Mishra M, Mishra RK, Chowdhuri DK (2010) Heat shock proteins in toxicology: how close and how far? Life Sci 86(11–12):377–384. https://doi.org/10.1016/j.lfs.2009.12.015
Hajihashemi S, Brestic M, Landi M et al (2020) Resistance of Fritillaria imperialis to freezing stress through gene expression, osmotic adjustment and antioxidants. Sci Rep 10:10427. https://doi.org/10.1038/s41598-020-63006-7
Hervieu F, Ledily F, Huault C, Billard JP (1995) Contribution of ornithine aminotransferase to proline accumulation in NaCl-treated radish cotyledons. Plant Cell and Environ 18(2):205–210. https://doi.org/10.1111/j.1365-3040.1995.tb00354.x
Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. The Plant J 61:1041–1052. https://doi.org/10.1111/j.1365-313X.2010.04124.x
Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucl Acids Res. https://doi.org/10.1093/nar/gkm259
Hossain A, Skalicky M, Brestic M, Maitra S, Ashraful Alam M, Syed MA, Hossain J, Sarkar S, Saha S, Bhadra P et al (2021) Consequences and mitigation strategies of abiotic stresses in wheat (Triticum aestivum L.) under the changing climate. Agronomy 11:241. https://doi.org/10.3390/agronomy11020241
Hu CA, Delauney AJ, Verma DP (1992) A bifunctional enzyme (delta 1-pyrroline-5-carboxylate synthetase) catalyzes the first two steps in proline biosynthesis in plants. PNAS 89(19):9354–9358. https://doi.org/10.1073/pnas.89.19.9354
Hruz T et al (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinform 2008:5. https://doi.org/10.1155/2008/420747
Hur J, Jung K-H, Lee C-H, An G (2004) Stress-inducible OsP5CS2 gene is essential for salt and cold tolerance in rice. Plant Sci 167:417–426. https://doi.org/10.1016/j.plantsci.2004.04.009
Islam T, Manna M, Kaul T (2015) Genome-wide dissection of Arabidopsis and rice for the identification and expression analysis of glutathione peroxidases reveals their stress-specific and overlapping response patterns. Plant Mol Biol Rep 33:1413–1427. https://doi.org/10.1007/s11105-014-0846-6
Islam F, Yasmeen T, Arif MS, Ali S, Ali B, Hameed S, Zhou W (2016) Plant growth promoting bacteria confer salt tolerance in Vigna radiata by up-regulating antioxidant defense and biological soil fertility. J Plant Growth Regul 80:23–36
Kaur G, Asthir B (2015) Proline: a key player in plant abiotic stress tolerance. Biol Plant 59:609–619. https://doi.org/10.1007/s10535-015-0549-3
Kavi Kishor PB, Sreenivasulu N (2014) Is proline accumulation per se correlated with stress tolerance or is proline homeostasis a more critical issue? Plant Cell Environ 37(2):300–311. https://doi.org/10.1111/pce.12157
Khaleghi A, Naderi R, Brunetti C, Maserti BE, Salami SA, Babalar M (2019) Morphological, physiochemical and antioxidant responses of Maclura pomifera to drought stress. Sci Rep 9(1):19250. https://doi.org/10.1038/s41598-019-55889-y
Khanna-Chopra R, Semwal V, Lakra N and Pareek A (2019) Proline – A key regulator conferring plant tolerance to salinity and drought. In: Plant tolerance to environmental stress, 1st edn. Taylor & Francis group, UK, pp 59–80
Kumar V, Shriram V, Hossain MA, Kavi Kishor PB (2015) Engineering proline metabolism for enhanced plant salt stress tolerance. In: Wani SH, Hussain MA (eds) Managing Salt Tolerance in Plants: Molecular and Genomic Perspectives, 1st edn. CRC Press/Taylor & Francis Group, Boca Raton FL, USA, pp 353–372
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096
Lei P, Xu Z, Liang J, Luo X, Zhang Y, Feng X et al (2016) Poly (g-glutamic acid) enhanced tolerance to salt stress by promoting proline accumulation in Brassica napus L. Plant Growth Regul 78:233–241. https://doi.org/10.1007/s10725-015-0088-0
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. Nucl Acids Res 30(1):325–327. https://doi.org/10.1093/nar/30.1.325
Li W, Brandriss MC (1992) Proline biosynthesis in Saccharomyces cerevisiae: molecular analysis of the PRO1 gene, which encodes gamma-glutamyl kinase. J Bacteriol 174:4148–4156. https://doi.org/10.1128/jb.174.12.4148-4156.1992
Liu Y, Wang L, Li Y, Li X, Zhang J (2019) Proline metabolism-related gene expression in four potato genotypes in response to drought stress. Biol Plant 63:757–764
Ma Y, Dias MC, Freitas H (2020) Drought and salinity stress responses and microbe-induced tolerance in plants. Front Plant Sci 11:591911. https://doi.org/10.3389/fpls.2020.591911Molazem
Molazem D, Bashirzadeh A (2015) Impact of salinity stress on proline reaction, peroxide activity and antioxidant enzymes in maize (Zea mays L.). Pol J Environ Stud 24(2):597–603
Mansour MMF, Ali EF (2017) Evaluation of proline functions in saline conditions. Phytochemistry 140:52–68. https://doi.org/10.1016/j.phytochem.2017.04.016
Nakashima K, Satoh R, Kiyosue T, Yamaguchi-Shinozaki K, Shinozaki K (1998) A gene encoding proline dehydrogenase is not only induced by proline and hypo-osmolarity, but is also developmentally regulated in the reproductive organs of Arabidopsis. Plant Physiol 118(4):1233–1241. https://doi.org/10.1104/pp.118.4.1233
Pérez-Llano Y, Rodríguez-Pupo EC, Druzhinina IS, Chenthamara K, Cai F, Gunde-Cimerman N, Zalar P, Gostinčar C, Kostanjšek R, Folch-Mallol JL, Batista-García RA, Sánchez-Carbente MDR (2020) Stress reshapes the physiological response of halophile fungi to salinity. Cells 9(3):525. https://doi.org/10.3390/cells9030525
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera-A visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. https://doi.org/10.1002/jcc.20084
Rasel M, Tahjib-Ul-Arif M, Hossain MA et al (2020) Screening of salt-tolerant rice landraces by seedling stage phenotyping and dissecting biochemical determinants of tolerance mechanism. J Plant Growth Regul. https://doi.org/10.1007/s00344-020-10235-9
Roosens NH, Thu TT, Iskandar HM, Jacobs M (1998) Isolation of the ornithine-d-aminotransferase cDNA and effect of salt stress on its expression in Arabidopsis thaliana. Plant Physiol 117(1):263–271. https://doi.org/10.1104/pp.117.1.263
Roosens NH, Bitar F, Loenders K, Angenon G, Jacobs M (2002) Overexpression of ornithine-delta-aminotransferase increases proline biosynthesis and confers osmotolerance in transgenic plants. Mol Breeding 9:73–80. https://doi.org/10.1023/A:1026791932238
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Shamsul H, Qaiser H, Mohammed N, Arif SW, John P, Aqil A (2012) Role of proline under changing environments. Plant Signal Behav 7(11):1456–1466. https://doi.org/10.4161/psb.21949
Shehzad MA, Nawaz F, Ahmad F, Ahmad N, Masood S (2020) Protective effect of potassium and chitosan supply on growth, physiological processes and antioxidative machinery in sunflower (Helianthus annuus L.) under drought stress. Ecotoxicol Environ Saf 187:109841. https://doi.org/10.1016/j.ecoenv.2019.109841
Strizhov N, Abraham E, Okresz L, Blickling S, Zilberstein A, Schell J, Koncz C, Szabados L (1997) Differential expression of two P5CS genes controlling proline accumulation during salt-stress requires ABA and is regulated by ABA1, ABI1 and AXR2 in Arabidopsis. Plant J 12(3):557–569. https://doi.org/10.1046/j.1365-313x.1997.00557.x
Szabados L, Savouré A (2010) Proline: a multifunctional amino acid. Trends Plant Sci 15:89–97. https://doi.org/10.1016/j.tplants.2009.11.009
Turchetto-Zolet AC, Margis-Pinheiro M, Margis R (2009) The evolution of pyrroline-5-carboxylate synthase in plants: a key enzyme in proline synthesis. Mol Genet Genomics 281(1):87–97. https://doi.org/10.1007/s00438-008-0396-4
Verbruggen N, Hermans C (2008) Proline accumulation in plants: a review. Amino Acids 35:753–759. https://doi.org/10.1007/s00726-008-0061-6
Verslues PE, Sharma S (2010) Proline metabolism and its implications for plant-environment interaction. Arabidopsis Book 8:e0140. https://doi.org/10.1199/tab.0140
Verslues PE, Agarwal M, Katiyar-Agarwal S, Zhu JH, Zhu JK (2006) Methods and concepts in quantifying resistance to drought, salt and freezing abiotic stresses that affect plant water status. Plant J 45(4):523–539. https://doi.org/10.1111/j.1365-313X.2005.02593.x
Wang H, Tang X, Hon W, Shao HB (2015) Proline accumulation and metabolism-related genes expression profiles in Kosteletzkya virginica seedlings under salt stress. Front Plant Sci 6:792. https://doi.org/10.3389/fpls.2015.00792
Wang X, Mao Z, Zhang J, Hemat M, Huang M, Cai J, Zhou Q, Dai T, Jiang D (2019) Osmolyte accumulation plays important roles in the drought priming induced tolerance to post anthesis drought stress in winter wheat (Triticum aestivum L.). Environ Exp Bot 166:103804. https://doi.org/10.1016/j.envexpbot.2019.103804
Winter G, Todd CD, Trovato M, Forlani G, Funck D (2015) Physiological implications of arginine metabolism in plants. Front Plant Sci 6:534. https://doi.org/10.3389/fpls.2015.00534
Wu LQ, Fan ZM, Guo L, Li YQ, Zhang WJ, Qu LJ, Chen ZL (2003) Over-expression of an Arabidopsis delta-OAT gene enhances salt and drought tolerance in transgenic rice. Chin Sci Bull 48:2594–2600
Yang SL, Lan SS, Gong M (2009) Hydrogen peroxide-induced proline and metabolic pathway of its accumulation in maize seedlings. J Plant Physiol 166(15):1694–1699. https://doi.org/10.1016/j.jplph.2009.04.006
Yifeng L, Chih-yu C, Alice MK, Wyeth WW (2015) The identification of cis-regulatory elements: a review from a machine learning perspective. BioSystems 138:6–17. https://doi.org/10.1016/j.biosystems.2015.10.002
You J, Hu H, Xiong L (2012) An ornithine δ-aminotransferase gene OsOAT confers drought and oxidative stress tolerance in rice. Plant Sci 197:59–69. https://doi.org/10.1016/j.plantsci.2012.09.002
Acknowledgements
SA acknowledge the Ministry of Science and Technology, Government of the People’s Republic of Bangladesh for providing NST fellowship. TI and SA acknowledge Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka the logistic support and laboratory facilities. TI designed the experiment and SA retrieved the data and prepared the manuscript. TI and SA analyzed the data.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Arabia, S., Shah, M.N.A., Sami, A.A. et al. Identification and expression profiling of proline metabolizing genes in Arabidopsis thaliana and Oryza sativa to reveal their stress-specific transcript alteration. Physiol Mol Biol Plants 27, 1469–1485 (2021). https://doi.org/10.1007/s12298-021-01023-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12298-021-01023-0