Ertuğrul FİLİZ, Hüseyin TOMBULOĞLU, Abdugaffar ABLAZOV

Genome-wide analysis of response to low sulfur (LSU) genes in grass species and expression profiling of model grass species Brachypodium distachyon under S deficiency

Sulfur (S) affects the plant life cycle and crop yield and has nutritional importance for human and animal diet. Its deficiency is one of the major problems in agriculture. However, the plant-specific LSU (response to Low Sulfur) gene family has not been extensively analyzed in major plant species such as grasses. In this study, we have performed in silico genome-wide analysis of LSU genes in 6 grass species, including Brachypodium distachyon, Sorghum bicolor, Oryza sativa, Zea mays, Triticum aestivum, and Panicum virgatum. All identified LSU genes contained one exon encoding proteins of acidic character with cytoplasmic localization. In silico analysis of cis-elements revealed that sulfur-responsive elements (SURE boxes, Sulfur Response Element, GAGAC motif) were present in all LSU genes. In phylogenetic analysis, dicot and monocot LSU genes were separated. Expression profiles of B. Distachyon BdLSU1 and BdLSU2 genes were analyzed by qRT-PCR method. Two Brachypodium LSU genes demonstrated different expression patterns when subjected to 48 h of S-depletion treatment. In roots, the BdLSU2 gene was upregulated, while BdLSU1 was downregulated. In leaves, expression levels were decreased for both genes. Analysis of the BdLSU expression under drought, cold, salt, and heat stresses was carried out based on the Brachypodium stress atlas. Results showed that BdLSU genes are not specific to S limitation; indeed, they may be involved in different stress conditions by cooperating with their interacting partner proteins. The results of this study could significantly contribute to the understanding of LSU genes in plants, particularly in grass species. These results may also support plant molecular studies by aiding the understanding of the sulfur assimilation pathway.

PDF

___

Buchner P, Takahashi H, Hawkesford MJ (2004). Plant sulphate transporters: co-ordination of uptake, intracellular and long-distance transport. J Exp Bot 55: 1765-1773.
Ciftci-Yilmaz S, Mittler R (2008). The zinc finger network of plants. Cell Mol Life Sci 65: 1150-1160.
Davidian JC, Kopriva S (2010). Regulation of sulfate uptake and assimilation - the same or not the same? Mol Plant 3: 314-325.
Davletova S, Schlauch K, Coutu J, Mittler R (2005). The zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol 139: 847-856.
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C et al. (2013). STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41: D808-D815.
Gallardo K, Courty PE, Signor CL, Wipf D, Vernoud V (2014). Sulfate transporters in the plant's response to drought and salinity: regulation and possible functions. Front Plant Sci 5: 580.
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: Walker JM, editor. The Proteomics Protocols Handbook. New York, NY, USA: Humana Press, pp. 571-607.
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Rokhsar DS (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40: D1178-D1186.
Guo AY, Zhu QH, Chen X, Luo JC (2007). GSDS: A gene structure display server. Yi Chuan 29: 1023-1026.
Hall TA (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid Symp Ser 41: 95-98.
Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297-300.
Hirai MY, Fujiwara T, Awazuhara M, Kimura T, Noji M, Saito K (2003). Global expression profiling of sulfur-starved Arabidopsis by DNA macroarray reveals the role of O-acetyl-l-serine as a general regulator of gene expression in response to sulfur nutrition. Plant J 33: 651-663.
Hoagland DR, Arnon DI (1950). The water-culture method for growing plants without soil. Calif Aes Bull 347: 1-39.
Honsel A, Kojima M, Haas R, Frank W, Sakakibara H, Herschbach C, Rennenberg H (2012). Sulphur limitation and early sulphur deficiency responses in poplar: significance of gene expression, metabolites, and plant hormones. J Exp Bot 63: 1873-1893.
Hubberten HM, Klie S, Caldana C, Degenkolbe T, Willmitzer L, Hoefgen R (2012). Additional role of O-acetylserine as a sulfur status independent regulator during plant growth. Plant J 70: 666-677.Hudson KA,
Hudson ME (2015). A classification of basic helix-loop-helix transcription factors of soybean. International Journal of Genomics 2015: 603182.
Kavas M, Baloğlu MC, Atabay ES, Ziplar UT, Daşgan HY, Ünver T (2016). Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. Mol Genet Genomics 291: 129-143.
Krishna SS, Majumdar I, Grishin NV (2003). Structural classification of zinc fingers. Nucleic Acids Res 31: 532-550.
Lewandowska M, Wawrzynska A, Kaminska J, Liszewska F, Sirko A (2005). Identification of novel proteins of Nicotiana tabacum regulated by short term sulfur starvation. In: Saito K, De Kok LJ, Stulen I, Hawkesford MJ, Schnug E, Sirko A, Rennenberg H, editors. Sulfur Transport and Assimilation in Plants in the Postgenomic Era. Leiden, the Netherlands: Backhuys Publishers, pp. 153-156.
Lewandowska M, Wawrzynska A, Moniuszko G, Lukomska J, Zientara K, Piecho M (2010). A contribution to identification of novel regulators of plant response to sulfur deficiency: characteristics of a tobacco gene UP9C, its protein product and the effects of UP9C silencing. Mol Plant 3: 347-360.
Licausi F, Ohme-Takagi M, Perata P (2013). APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. New Phytol 199: 639-649.
Liu W, Tai H, Li S, Gao W, Zhao M, Xie C, Li WX (2014). bHLH122 is important for drought and osmotic stress resistance in Arabidopsis and in the repression of ABA catabolism. New Phytol 201: 1192-1204.
Maruyama-Nakashita A, Nakamura Y, Watanabe-Takahashi A, Inoue E, Yamaya T, Takahashi H (2005). Identification of a novel cis-acting element conferring sulfur deficiency response in Arabidopsis roots. Plant J 42: 305-314.
Mignone F, Gissi C, Liuni S, Pesole G (2002). Untranslated regions of mRNAs. Genome Biol 3: 1-10.
Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012). AP2/ERF family transcription factors in plant abiotic stress responses. BBA-Gene Regul Mech 1819: 86-96.
Moniuszko G, Skoneczny M, Zientara-Rytter K, Wawrzyńska A, Głów D, Cristescu SM, Harren FJ, Sirko A (2013). Tobacco LSU-like protein couples sulphur-deficiency response with ethylene signalling pathway. J Exp Bot 64: 5173-5182.
Nikiforova V, Freitag J, Kempa S, Adamik M, Hesse H, Hoefgen R (2003). Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. Plant J 33: 633-650.
Nikiforova VJ, Daub CO, Hesse H, Willmitzer L, Hoefgen R (2005). Integrative genemetabolite network with implemented causality deciphers informational fluxes of sulphur stress response. J Exp Bot 56: 1887-1896.
Ohme-Takagi M, Shinshi H (1995). Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7: 173-182.
Omranian N, Mueller-Roeber B, Nikoloski Z (2012). PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana. Mol Biosyst 8: 1121-1127.
Pfaffl MW (2001). A new mathematical model for relative quantification in real time RT-PCR. Nucleic Acids Res 29: 2002-2007.
Pires N, Dolan L (2010). Origin and diversification of basic-helix-loop-helix proteins in plants. Mol Biol Evol 27: 862-874.
Priest HD, Fox SE, Rowley ER, Murray JR, Michael TP, Mockler TC (2014). Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress. PLoS One 9: e87499.
Riechmann JL, Meyerowitz EM (1998) The AP2/EREBP family of plant transcription factors. Biol Chem 379: 633-646.
Saito K (2004). Sulfur assimilatory metabolism. The long and smelling road. Plant Physiol 136: 2443-2450.
Sirko A, Wawrzynska A, Rodríguez MC, Sektas P (2015). The family of LSU-like proteins. Front Plant Sci 5: 1-9.
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
Takahashi H, Kopriva S, Giordano M, Saito K, Hell R (2011). Sulfur assimilation in photosynthetic organisms: molecular functions and regulations of transporters and assimilatory enzymes. Annu Rev Plant Biol 62: 157-184.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30: 2725-2729.
Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
Timothy L, Mikael Bodén B, 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: 202-208.
Tombuloglu H, Semizoglu N, Sakcali S, Kekec G (2012). Boron induced expression of some stress-related genes in tomato. Chemosphere 86: 433-438.
Usadel B, Blasing OE, Gibon Y, Retzlaff K, Hohne M, Gunther M, Stitt M (2008). Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes. Plant Physiol 146: 1834-1861.
Wang Y, Zhang WZ, Song LF, Zou JJ, Su Z, Wu WH (2008). Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol 148: 1201-1211.
Wawrzynska A, Lewandowska M, Hawkesford MJ, Sirko A (2005). Using a suppression subtractive library-based approach to identify tobacco genes regulated in response to short-term Sulphur deficit. J Exp Bot 56: 1575-1590.
Wawrzynska A, Lewandowska M, Sirko A (2010). Nicotiana tabacumEIL2 directly regulates expression of at least one tobacco gene induced by sulphur starvation. J Exp Bot 61: 889-900.
Yu CS, Chen YC, Lu CH, Hwang JK (2006). Prediction of protein subcellular localization. Proteins 64: 643-651.
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004). GENEVESTIGATOR. Arabidopsis microarray database and analysis tool box. Plant Physiol 136: 2621-2632.
Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, Gruissem W (2008). Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Mol Plant 1: 851-857.