Bioinformatic and empirical analysis of a gene encoding serine/threonine protein kinase regulated in response to chemical and biological fertilizers in two maize (Zea mays L.) cultivars

Document Type: Original article

Authors

1 Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Shiraz, Iran

2 Plant Breeding and Biotechnology Department, Agricultural Sciences and Natural Resources University of Sari, Sari, Iran

Abstract

Molecular structure of a gene, ZmSTPK1, encoding a serine/threonine protein kinase in maize was analyzed by bioinformatic tool and its expression pattern was studied under chemical biological fertilizers. Bioinformatic analysis cleared that ZmSTPK1 is located on chromosome 10, from position 141015332 to 141017582. The full genomic sequence of the gene is 2251 bp in length and includes 2 exons. Its cDNA length is 1900 bp with a 5'-untranslated region of 311 bp and 3'-untranslated region of 341 bp, of which 1248 bp from open reading frame encoding 415 amino acid residues with a molecular weight of 46 kDa and an isoelectric point 7.2. Also, an upstream open reading frame contains 100 aa was found at -12 position from ATG initiation codon. ZmSTPK1 with a long half-life, 10 hours in Escherichia coli, and instability index of 32.25 is classified as a stable protein. A calmodulin binding domain was found in ZmSTPK1 at position from 395 to 405 in C-terminal end. The helical wheel analysis showed that the stretch of residues Ile-395 to Asp-415 has the potential to form a charged amphiphilic a-helix characteristic of a calmodulin-binding region. Two P1BS-like motifs, which are present in the promoter regions of Pi starvation-induced genes, were located at positions -48 and -867 from ATG initiation codon. The expression of ZmSTPK1 responded to available phosphate, and its expression up-regulated under phosphate starvation

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1. Hurni S, Scheuermann D, Krattinger SG, Kessel B, Wicker T, Herren G, Fitze MN, Breen J, Presterl T, Ouzunova M, Keller B. The maize disease resistance gene Htn1 against northern corn leaf blight encodes a wall-associated receptor-like kinase. Proc Natl Acad Sci USA 2015;112:8780-8785.

2. Liu J, Maldonado-Mendoza I, Lopez-Meyer M, Cheung F, Town CD, Harrison MJ. Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots. Plant J 2007;50:529-544.

3. Richardson AE, Barea JM, McNeill AM, Prigent-Combaret C. Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 2009;321:305-339.

4. Salvioli Al, Zouari I, Chalot M, Bonfante P. The arbuscular mycorrhizal status has an impact on the transcriptome profile and amino acid composition of tomato fruit. BMC Plant Biol 2012;12:44.

5. Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S. The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 2012;488: 535-539.

6. Wan B, Lin Y, Mou T. Expression of rice Ca2+-dependent protein kinases (CDPKs) genes under different environmental stresses. FEBS Lett 2007;581:1179-1189.

7. Pingali P. Green revolution: impacts, limits, and the path ahead. Proc Natl Acad Sci USA 2012;109:12302-12308.

8. Ventura C, Maioli M. Protein kinase C control of gene expression. Crit Rev Eukar Gene 2001;11:243-267.

9. Romeis T, , Ludwig AA, Martin R, Jones JDG. Calcium‐dependent protein kinases play an essential role in a plant defence response. EMBO J 2001;20:5556-5567.

10. Korj T, Rudd JJ, Nurnberger T, Gabler Y, Lee J, Scheel D. Mitogen-activated protein kinases play an essential role in oxidative burst-independent expression of pathogenesis-related genes in parsley. J Biol Chem 2003;278:2256-2264.

11. Afzal AJ, Wood AJ, Lightfoot DA. Plant receptor-like serine threonine kinases: Roles in signaling and plant defense. Mol Plant Microbe In 2008;21:507-517.

12. Tagliabracci VS, Pinna LA, Dixon JE. Secreted protein kinases. Trends Biochem Sci 2013:38:121-130.

13. Sanchez L, Weidmann S, Arnould C, Bernard AR, Gianinazzi S, Gianinazzi-Pearson V. Pseudomonas fluorescens and Glomus mosseae trigger DMI3-dependent activation of genes related to a signal transduction pathway in roots of Medicago truncatula. Plant Physiol 2005;139:1065-1077.

14. Güimil S, Chang HS, Zhu T, Sesma A, Osbourn A, Roux C, Loannidis V, Oakeley EJ, Docquier P, Descombes P, Briggs SP, Paszkowski U. Comparative tran- scriptomics of rice reveals an ancient pattern of response to microbial colonization. Proc Natl Acad Sci USA 2005;102:8066-8070.

15. Hohnjec N, Vieweg MF, Puhler A, Becker A, Kuster H. Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza. Plant Physiol 2005;137:1283-1301.

16. Parniske M. Molecular genetics of the arbuscular mycorrhizal symbiosis. Curr Opin  Plant Biol 2004;7:414-421.

17. Liu J, Blaylock L, Endre G, Cho J, Town CD, VandenBosch K, Harrison MJ.Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of the arbuscular mycorrhizal symbiosis. Plant Cell 2003;15:2106-2123.

18. Paszkowski U. Mutualism and parasitism: the yin and yang of plant symbioses. Curr Opin Plant Biol 2006;9:364-370.

19. Manthey K, Krajinski F, Hohnjec N, Firnhaber C, Puhler A, Perlick AM, Kuster H. Transcriptome profiling in root nodules and arbuscular mycorrhiza identifies a collection of novel genes induced during Medicago truncatula root endosymbioses. Mol Plant Microbe Interact 2004;17:1063-1077.

20. Rentel MC,Lecourieux D, Ouaked F, Usher SL, Petersen L, Okamoto H, Knight H, Peck SC, Grierson CS, Hirt H, Knight MR. OXI1 kinase is necessary for oxidative burst-mediated signalling in Arabidopsis. Nature 2004;427:858-861.

21. Rastgoo L, Alemzadeh A. Biochemical responses of gouan (Aeluropus littoralis) to heavy metals stress. Aust J Crop Sci 2011;5:375-383.

22. Deng Y, Chen K, Teng W, Zhan A, Tong Y, Feng G, Cui Z, Zhang F, Chen X. Is the inherent potential of maize roots efficient for soil phosphorus acquisition? PLoS One 2014;9:e90287.

23. Saghai Maroof MA, Soliman KM, Jorgensen R, Allard RW. Ribosomal DNA spacer length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 1984;81:8014-8018.

24. Sarmadi L, Alemzadeh A, Ghareyazie B. PCR-based detection of genetically modified soybean at a grain receiving port in Iran. J Agr Sci Tech 2016;18:805-815.

25. Esmaeili Tazangi S, Alemzadeh A, Tale AM, Jam M. Expression pattern of AlNHA1 in Aeluropus littoralis under heavy metals stress. Plant Cell Biotech Mol Biol 2015; 16:145-154.

26. Alemzadeh A, Fujie M, Usami S, Yamada T. Isolation of high-quality RNA from high-phenolic tissues of eelgrass (Zostera marina L.) by keeping temperature low. Plant Mol Biol Rep 2005;23:421a-421h.

27. Lescot M, Déhais P, Moreau Y, De Moor B, Rouzé, P, Rombauts, S. PlantCARE: a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 2002;30:325-327.

28. Padgett RA, Grabowski PJ, Konarska MM, Seiler S, Sharp PA. Splicing of messenger RNA precursors. Annu Rev Biochem 1986;55:1119-1150.

29. Arango M, Gévaudant F, Oufattole M, Boutry M. The plasma membrane proton pump ATPase: the significance of gene subfamilies. Planta 2003;216:355-365.

30. Sami Z, Alemzadeh A. Isolation and molecular characterization of a novel Na+/H+ antiporter gene, AlNHX2, from Aeluropus littoralis and comparison of AlNHX1 and AlNHX2. Plant OMICS 2016;9:205-212.

31. Oja V, Savchenko G, Burkhard J, Heber U. pH and buffer capacities of apoplastic and cytoplasmic cell compartments in leaves. Planta 1999;209:239-249.

32. Tursun B, Schlüter A, Peters MA, Viehweger B, Ostendorff HP, Soosairajah J, Drung A, Bossenz M, Johnsen SA, Schweizer M, Bernard O, Bach I. The ubiquitin ligase Rnf6 regulates local LIM kinase 1 levels in axonal growth cones. Genes Dev 2005;19:2307-2319.

33. Bähler M, Rhoads A. Calmodulin signaling via the IQ motif. FEBS Lett 2002;513: 107-113.

34. Snedden WA, Fremm H. Calmodulin as a versatile calcium signal transducer in plants. New Phytol 2001;151:35-66.

35. Kang CH, Jung WY,  Kang YH, Kim JY, KimDG Jeong JC, Baek DW, Jin JB, Lee JY, Kim MO, Chung WS, Mengiste T, Koiwa H, KwakSS, Bahk JD, Lee SY, Nam JS,  Yun DJ, Cho MJ. AtBAG6, a novel calmodulin-binding protein, induces programmed cell death in yeast and plants. Cell Death Differ 2005;13:84-95.

36. Rubio V, Linhares F, Solano R, Martin AC, Iglesias J, Leyva A, PazAres J. A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev 2001;15:2122-2133.

37. Wu P, Shou H, Xu G, Lian X. Improvement of phosphorus efficiency in rice on the basis of understanding phosphate signaling and homeostasis. Curr Opin Plant Biol 2013;16:205-212.

38. Bustos R, Castrillo G, Linhares F, Puga MI, Rubio V, Pérez-Pérez J, Solano R, Leyva A, Paz-Ares J. A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis. PLoS Genet 2010;e1001102.

39. Li LH, Guo N, Wu ZY, Zhao JM, Sun JT, Wang XT, Xing H. P1BS, a conserved motif involved in tolerance to phosphate starvation in soybean. Genet Mol Res 2015; 14:9384-9394.