با همکاری مشترک دانشگاه پیام نور و انجمن بیوتکنولوژی جمهوری اسلامی ایران

نوع مقاله : علمی پژوهشی

نویسندگان

1 دانش‌آموخته کارشناسی‌ارشد بیوتکنولوژی کشاورزی، دانشکده علوم کشاورزی، دانشگاه گیلان، رشت، ایران.

2 دانشیار، گروه بیوتکنولوژی کشاورزی، دانشکده علوم کشاورزی، دانشگاه گیلان، رشت، ایران.

3 دانش‌آموخته دکترای بیوتکنولوژی کشاورزی-گیاهی، دانشکده علوم کشاورزی، دانشگاه گیلان، رشت، ایران.

چکیده

پروتئین‌های خانواده آنتی‌پورتر یون کلسیم/کاتیون (CaCA) نقش حیاتی در هموستازی یون کلسیم دارند که یک رویداد مهم در طول نمو و پاسخ دفاعی گیاه است. در مطالعه حاضر با استفاده از داده‌های بانک‌های اطلاعاتی مرتبط، 14 ژن CaCAs در ژنوم ذرت شناسایی و براساس سازماندهی ساختاری و ارتباط تکاملی آن‌ها با پروتئین‌های شناسایی‌شده به سه گروه CAX، CCX و MHX طبقه‌بندی شدند. بیشتر پروتئین‌های ZmCaCA دارای دو دمین Na_Ca_ex بودند. تمامی ژن‌های شناسایی‌شده دارای حداقل یک موتیف کارکردی بوده و ساختار ژنی هر زیر گروه CaCA بسیار حفاظت‌ شده است. در پیش‌بینی مولکول-های miRNA واکنش‌گر نسبت به ژن‌های CaCA در ذرت 33 نوع miRNA متفاوت شناسایی شد که در تنظیم بیان پس از رونویسی 13 ژن CaCAs از طریق برش mRNA یا ممانعت از ترجمه دخالت دارند. علاوه بر این، چندین عنصر تنظیمی cis پاسخ به تنش‌ها و هورمون‌ها در پیش‌بر این ژن‌ها شناسایی شد. بیان متغیر اکثر ژن‌های ZmCaCA در مراحل مختلف رشد و نمو، نقش مشخص آن‌ها در نمو ذرت را نشان می-دهد. همچنین القاء بیان این ژن‌ها در پاسخ به تنش‌های غیر زیستی (سرما، شوری، خشکی) کارکرد دفاعی ژن‌های ZmCaCA را مشخص نمود. بیشترین افزایش و کاهش بیان ژن مربوط به ژن‌های CAX است. نتایج این مطالعه اطلاعات پایه در مورد روابط فیلوژنی و کارکردهای احتمالی ژن‌های CaCA ذرت را برای پژوهش‌های آتی فراهم می‌سازد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Bioinformatical study of Calcium/cation (CaCA) antiporters gene family in maize (Zea mays L.)

نویسندگان [English]

  • Behnaz Karami Lake 1
  • Mohammad Sohani 2
  • Amin Abedi 3

1 M.Sc. Graduated, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

2 Associate Professor, Department of Agricultural Biotechnology, Faculty of Agriculture Science, University of Guilan, Rasht. Iran

3 PhD Graduated, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

چکیده [English]

The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. In the present study, using related database, 14 CaCA genes were identified in the maize genome and classified according to their structural organization and evolutionary association with the identified CAX, CCX and MHX proteins. Most of the ZmCaCA proteins had two Na_Ca_ex domains. All of the identified genes had at least one functional motif and gene structure of each CaCA subgroup is highly conserved. In the prediction of reactive miRNAs relative to CaCA genes in maize, 33 different miRNA variants were identified that regulate the expression of 13 CaCA genes through cleavage or inhibition of translation. In addition, several cis-acting regulatory elements in ZmCaCA genes were found to be related to hormones stress responses. The variable expression of most ZmCaCA genes at different stages of development indicates their distinct role in development. Expression of these genes in abiotic stresses (cold, salt, and drought) indicates their role in stress response. The greatest high expression and down regulation of gene expression is related to CAX genes. The results of this study provide basic data about phylogeny and putative function of these genes for future studies on the role of CaCA genes in maize.

کلیدواژه‌ها [English]

  • Bioinformatics
  • Microarray
  • Phylogenetic analysis
  • Promoter
Amagaya K, Shibuya T, Nishiyama M, Kato K, Kanayama Y (2020) Characterization and Expression Analysis of the Ca2+/Cation Antiporter Gene Family in Tomatoes. Plants 9 (1): 25.
Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, De Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E (2012) ExPASy: SIB bioinformatics resource portal. Nucleic acids res. 40 (W1): W597-W603.
Axelsen KB, Palmgren MG (2001) Inventory of the superfamily of P-type ion pumps in Arabidopsis. Plant physiol. 126 (2): 696-706.
Bailey TL, Boden M, 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 (suppl_2): W202-W208.
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths‐Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL (2004) The Pfam protein families database. Nucleic acids res. 32 (suppl_1): D138-D141.
Bickerton PD, Pittman JK (2015) Role of cation/proton exchangers in abiotic stress signaling and stress tolerance in plants. In: Elucidation of Abiotic Stress Signaling in Plants. Springer, pp 95-117.
Bolser D, Staines DM, Pritchard E, Kersey P (2016) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. In: Plant bioinformatics. Springer, pp 115-140.
Case RM, Eisner D, Gurney A, Jones O, Muallem S, Verkhratsky A (2007) Evolution of calcium homeostasis: from birth of the first cell to an omnipresent signalling system. Cell calcium. 42 (4-5): 345-350.
Corso M, Doccula FG, de Melo JRF, Costa A, Verbruggen N (2018) Endoplasmic reticulum-localized CCX2 is required for osmotolerance by regulating ER and cytosolic Ca2+ dynamics in Arabidopsis. Proc. Natl. Acad. Sci. 115 (15): 3966-3971.
Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic acids res. 39 (suppl_2): W155-W159.
Demidchik V, Shabala S, Isayenkov S, Cuin TA, Pottosin I (2018) Calcium transport across plant membranes: mechanisms and functions. New Phyto. 220 (1): 49-69.
Dinh H, Rajasekaran S (2013) PMS: a panoptic motif search tool. PloS one 8 (12).
Dodd AN, Kudla J, Sanders D (2010) The language of calcium signaling. Annu. Rev. Plant Biol. 61: 593-620.
Edmond C, Shigaki T, Ewert S, Nelson MD, Connorton JM, Chalova V, Noordally Z, Pittman JK (2009) Comparative analysis of CAX2-like cation transporters indicates functional and regulatory diversity. Biochem. J. 418 (1): 145-154.
Emery L, Whelan S, Hirschi KD, Pittman JK (2012) Protein phylogenetic analysis of Ca2+/cation antiporters and insights into their evolution in plants. Frontiers in plant science 3: 1.
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol. 39 (4): 783-791.
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic acids res. 39 (suppl_2): W29-W37.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J (2014) Pfam: the protein families database. Nucleic acids res. 42 (D1): D222-D230.
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: The proteomics protocols handbook. Springer, pp 571-607.
Gertz EM, Yu YK, Agarwala R, Schäffer AA, Altschul SF (2006) Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC biol. 4 (1): 41.
Giladi M, Shor R, Lisnyansky M, Khananshvili D (2016) Structure-functional basis of ion transport in sodium–calcium exchanger (NCX) proteins. Int. J. Mol. 17 (11): 1949.
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N (2012) Phytozome: a comparative platform for green plant genomics. Nucleic acids res. 40 (D1): D1178-D1186.
Hirschi KD (2004) The calcium conundrum. Both versatile nutrient and specific signal. Plant physiol. 136 (1): 2438-2442.
Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR (2019) An updated gene atlas for maize reveals organ‐specific and stress‐induced genes. PLANT J. 97 (6): 1154-1167.
Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G (2015) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 31 (8): 1296-1297.
Kader MA, Lindberg S, behavior (2010) Cytosolic calcium and pH signaling in plants under salinity stress. Plant signal. behav. 5 (3): 233-238.
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 6 (1): 4.
Klee EW, Ellis LB (2005) Evaluating eukaryotic secreted protein prediction. BMC bioinformatics 6 (1): 256.
Krogh A, Larsson B, Von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305(3): 567-80.
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33 (7): 1870-1874.
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic acids res. 40 (D1): D1202-D1210.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. bioinformatics. 23 (21): 2947-2948.
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. Nucleic acids res. 30 (1): 325-327.
Letunic I and Bork P (2018) 20 years of the SMART protein domain annotation resource. Nucleic acids res. 46(D1): D493-D496.
Li D, Liu Z, Gao L, Wang L, Gao M, Jiao Z, Qiao H, Yang J, Chen M, Yao L (2016) Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L. PloS one. 11 (4).
Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR (2010) The developmental dynamics of the maize leaf transcriptome. Nat. Genet. 42 (12): 1060.
Li P, Zhang G, Gonzales N, Guo Y, Hu H, Park S, Zhao J (2016) Ca2+‐regulated and diurnal rhythm‐regulated Na+/Ca2+ exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis. Plant, cell environ. 39 (2): 377-392.
Li Z, Wang X, Chen J, Gao J, Zhou X, Kuai B (2016) CCX1, a putative Cation/Ca2+ exchanger, participates in regulation of reactive oxygen species homeostasis and leaf senescence. Plant Cell Physiol. 57 (12): 2611-2619.
Manohar M, Shigaki T, Hirschi K (2011) Plant cation/H+ exchangers (CAXs): biological functions and genetic manipulations. Plant biol 13(4):561-569.
Navarro-León E, Ruiz JM, Albacete A, Blasco B (2019) Effect of CAX1a TILLING mutations and calcium concentration on some primary metabolism processes in Brassica rapa plants. J. Plant Physiol. 237: 51-60.
Park S, Elless MP, Park J, Jenkins A, Lim W, Chambers Iv E, Hirschi KD (2009) Sensory analysis of calcium‐biofortified lettuce. Plant Biotechnol. J. 7 (1): 106-117.
Paulsen IT, Nguyen L, Sliwinski MK, Rabus R, Saier Jr MH (2000) Microbial genome analyses: comparative transport capabilities in eighteen prokaryotes. J. Mol. Biol. 301 (1): 75-100.
Pittman JK (2011) Vacuolar Ca2+ uptake. Cell calcium 50 (2): 139-146.
Pittman JK, Hirschi KD (2016) Phylogenetic analysis and protein structure modelling identifies distinct Ca2+/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species. Rice. 9 (1): 3.
Qiao K, Wang F, Liang S, Hu Z, Chai T (2019) Heterologous expression of TuCAX1a and TuCAX1b enhances Ca2+ and Zn2+ translocation in Arabidopsis. Plant Cell Rep. 38 (5): 597-607.
Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 34 (2): 374-8.
Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, De Leon N, Kaeppler SM (2011) Genome‐wide atlas of transcription during maize development. Plant J. 66 (4): 553-563.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape a software environment for integrated models of biomolecular interaction networks. Genome res. 13 (11): 2498-504.
Shaul O, Hilgemann DW, de‐Almeida‐Engler J, Van Montagu M, Inzé D, Galili G (1999) Cloning and characterization of a novel Mg2+/H+ exchanger. EMBO J. 18(14):3973-3980.
Singh A, Roy S, Singh S, Das SS, Gautam V, Yadav S, Kumar A, Singh A, Samantha S, Sarkar AK (2017) Phytohormonal crosstalk modulates the expression of miR166/165s, target Class III HD-ZIPs, and KANADI genes during root growth in Arabidopsis thaliana. Sci. rep. 7 (1): 1-13.
Spalding EP, Harper JF (2011) The ins and outs of cellular Ca2+ transport. Curr. Opin. Plant Biol. 14 (6): 715-720.
Taneja M, Tyagi S, Sharma S, Upadhyay SK (2016) Ca2+/cation antiporters (CaCA): identification, characterization and expression profiling in bread wheat (Triticum aestivum L.). Front. plant sci. 7: 1775.
Tuteja N, Mahajan S (2007) Calcium signaling network in plants: an overview. Plant signaling behav. 2 (2): 79-85.
Umate P (2010) microRNA access to the target helicases from rice. Plant signaling behavior 5 (10): 1171-1175.
Vaid N, Pandey PK, Tuteja N (2012) Genome-wide analysis of lectin receptor-like kinase family from Arabidopsis and rice. Plant Mol. Biol. 80 (4-5): 365-388.
Wijaya E, Rajaraman K, Yiu SM, Sung WK (2007) Detection of generic spaced motifs using submotif pattern mining. Bioinformatics. 23 (12): 1476-85.
Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins: Structure, Function, Bioinformatics 64(3):643-651.
Zeng L, Deng R, Guo Z, Yang S, Deng X (2016) Genome-wide identification and characterization of Glyceraldehyde-3-phosphate dehydrogenase genes family in wheat (Triticum aestivum). BMC genomics. 17 (1): 240.
Zhang L, Chia J-M, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D (2009) A genome-wide characterization of microRNA genes in maize. PLoS genet. 5 (11).
Zhang L, Du L, Poovaiah B (2014) Calcium signaling and biotic defense responses in plants. Plant Signal Behav. 9 (11): e973818.
Zhou S, Ma S, Li M, Li C, Gong X, Guan Q, Tan Y, Shao Y, Li C, Ma F (2016) Comprehensive genomic analysis and expression profiling of Argonaute gene family and examination of their regulatory roles in water-use efficiency and abiotic stress responses in apple. Acta Physiol. Plant. 38 (9): 231.
Zhou X, Li S, Zhao Q, Liu X, Zhang S, Sun C, Fan Y, Zhang C, Chen R (2013) Genome-wide identification, classification and expression profiling of nicotianamine synthase (NAS) gene family in maize. BMC genomics 14 (1): 238.