مطالعه بیوانفورماتیکی پروتئین کینازهای وابسته به کلسیم (CPK) در گیاه آلوروپوس لیتورالیس (Aeluropus littoralis L.)

نوع مقاله : علمی پژوهشی

نویسندگان

1 دانشجوی کارشناسی‌ارشد بیوتکنولوژی کشاورزی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ایران

2 دانشیار، گروه بیوتکنولوژی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، ایران.

3 استاد، گروه مهندسی ژنتیک و بیولوژی، پژوهشکده ژنتیک و زیست‌فناوری کشاورزی طبرستان، دانشگاه علوم کشاورزی و منابع طبیعی ساری ، ایران.

4 استادیار، گروه مهندسی ژنتیک و بیولوژی، پژوهشکده ژنتیک و زیست‌فناوری کشاورزی طبرستان، دانشگاه علوم کشاورزی و منابع طبیعی ساری ، ایران.

چکیده

پروتئین کیناز وابسته به کلسیم (CPK) به عنوان عضوی از ابرخانواده کینازهای Ser/Thr، نقشی حیاتی در پاسخ و سازگاری به تنش‌ دارد. گیاه هالوفیت، Aeluropus littoralis، به عنوان یک مدل ارزشمند برای بهبود منابع ژنتیکی گیاهان زراعی و تحقیقات ژنومیکس تنش مورد توجه می‌باشد. به منظور شناسایی خانواده ژنی CPK در گیاه آلوروپوس لیتورالیس (AlCPK)، از داده‌های ژنومی برای تجزیه و تحلیل روابط فیلوژنتیک، ساختار اگزون/ اینترون، سازماندهی موتیف‌ها/ دامنه‌ها و پیش‌بینی شبکه‌های برهم‌کنش پروتئین- پروتئین استفاده شد. 14 ژن AlCPK در این گیاه شناسایی شد که از همولوژی بالایی با نه ژن آرابیدوپسیس تالیانا برخوردار بودند. بررسی اعضای خانواده ژنی AlCPK در پایگاه‌های اختصاصی دمین نشان داد که همه ژن‌های مورد بررسی (به‌جز AlCPK29.2) با توجه به دارا بودن چند دمین EF-hand و Kinase به خانواده ژنی CPK تعلق دارند. پروتئین AlCPK29.2 دارای کمترین وزن مولکولی و شاخص آلیفاتیک، بیشترین شاخص ناپایداری و هیدروپاتی در بین پروتئین‌های مورد بررسی بوده است. تجزیه و تحلیل ساختار ژنی نشان داد که بیشتر AlCPK‌ها ( 8/69 %) بیش از هفت اگزون برخوردارند. پروتئین AlCPK8 دارای دو موتیف میریستویلاسیون و دو موتیف پالمیتوئیلاسیون بود، پروتئین CPK34.1 فاقد موتیف میریستویلاسیون و پالمیتوئیلاسیون و پروتئین AlCPK5.1 دارای سه موتیف پالمیتوئیلاسیون می‌باشد. بیان مقایسه‌ای 34 عضو خانواده ژنی AtCPK در پنج تنش غیرزنده نشان داد که اعضای خانواده ژنی در سطوح مختلف کنترل و تنش از بیان متفاوتی برخوردار بودند که می‌تواند دلیلی بر بیان بافت- اختصاصی و البته تنش- اختصاصی اعضای این خانواده ‌باشد. ژن ABF4 به عنوان یکی از اجزای پیام‌رسان ABA، در بررسی تعاملات پروتئین-پروتئین اعضای خانواده AlCPK شناسایی گردید. نتایج این تحقیق می‌تواند در مطالعات بیان ژن‌های AlCIPK تحت تنش‌های غیرزیستی مختلف به منظور شناسایی عملکردها و سازکارهای پاسخ‎ به تنش سودمند باشد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Bioinformatics analysis of calcium-dependent protein kinase (CPK) in Aeluropus littoralis L.

نویسندگان [English]

  • Mozhdeh Arab 1
  • Hamid Najafi zarrini 2
  • Ghorbanali Nematzadeh 3
  • Seyyed Hamidreza Hashemi-petroudi 4
1 M.Sc. Student in Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
2 Associated Professor, Department of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.
3 Professor, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)
4 Assistant Professor, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)
چکیده [English]

Calcium-dependent protein kinase (CPK), as a member of Ser/Thr kinases superfamily, plays a vital role in responding and adapting to biotic and abiotic stresses. The halophyte plant, Aeluropus littoralis, has been considered an attractive model to improve genetic resources of crops and plant stress genomic research. In order to identify the A. littoralis CPK gene family, the whole genome sequences were used to analyze the phylogenetic relationships, exon/intron structure, protein motif/domain organization and the prediction of protein-protein interaction networks. Fourteen AlCPK genes were identified in A. littoralis that were homologous to nine Arabidopsis thaliana CPK genes. The protein domain analysis of AlCPK showed that all studied genes belong to the CPK family due to having several EF-hand (except for AlCPK29.2, which does not have an EF-hand domain) and Kinase domains. AlCPK29.2 protein had the lowest molecular weight and aliphatic index, the highest instability index and gravy among the studied proteins. Gene structure analysis showed that most of AlCPKs (69.8%) have more than seven exons. Besides, AlCPK8 protein was predicted with two N-myristoylation and two palmitoylation motifs, while CPK34.1 protein lacked N-myristoylation, and palmitoylation motif and AlCPK5.1 protein had three palmitoylation motifs. Transcriptome analysis of 34 members of the AtCPK gene family in five abiotic stresses showed that AtCPK genes had diverse expression at different treatments, which could be evidence for AtCPK tissue/ stress-specific expression. The ABF4 gene was identified as one of the components of ABA signaling in AlCPK protein-protein interactions. The findings of this research can be used to classify the roles and pathways of the stress response by studying AlCIPK gene expression under different abiotic stresses.

کلیدواژه‌ها [English]

  • Genomic-wide analysis
  • calcium sensors
  • CDPK
  • gene network
  • kinases

مراجع

Ahmadizadeh M, Chen J-T, Hasanzadeh S, Ahmar S, Heidari P (2020) Insights into the genes involved in the ethylene biosynthesis pathway in Arabidopsis thaliana and Oryza sativa. Journal of Genetic Engineering and Biotechnology. 18(1): 1-20.
Ahmed B, Alam M, Hasan F, Emdad EM, Islam S, Rahman N (2020) Jute CDPK genes and their role in stress tolerance and fiber development: A genome-wide bioinformatic investigation of Chorchorus capsularis and C. olitorius. Plant Gene. 24: 100252.
Asano T, Tanaka N, Yang G, Hayashi N, Komatsu S (2005) Genome-wide identification of the rice calcium-dependent protein kinase and its closely related kinase gene families: comprehensive analysis of the CDPKs gene family in rice. Plant and Cell Physiology. 46(2): 356-366.
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: 202-208.
Bi Z, Wang Y, Li P, Sun C, Qin T, Bai J (2021) Evolution and expression analysis of CDPK genes under drought stress in two varieties of potato. Biotechnology Letters. 43(2): 511-521.
Campo S, Baldrich P, Messeguer J, Lalanne E, Coca M, San Segundo B (2014) Overexpression of a calcium-dependent protein kinase confers salt and drought tolerance in rice by preventing membrane lipid peroxidation. Plant physiology. 165(2): 688-704.
Choi H-I, Park H-J, Park JH, Kim S, Im M-Y, Seo H-H, Kim Y-W, Hwang I, Kim SY (2005) Arabidopsis calcium-dependent protein kinase AtCPK32 interacts with ABF4, a transcriptional regulator of abscisic acid-responsive gene expression, and modulates its activity. Plant Physiology. 139(4): 1750-1761.
Crizel RL, Perin EC, Vighi IL, Woloski R, Seixas A, Da Silva Pinto L, Rombaldi CV, Galli V (2020) Genome-wide identification, and characterization of the CDPK gene family reveal their involvement in abiotic stress response in Fragaria x ananassa. Scientific Reports. 10(1): 1-17.
Dezhsetan S, Behnamian M, Fathi Ajirlou S, Ebrahimi MA, Yazdani B (2018) Identification, classification and bioinformatics expression analysis of NAC transcription factor gene family in Hordeum vulgare cv. Morex genome. Crop Biotechnology. 8(21): 17-35.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A (2019) The Pfam protein families database in 2019. Nucleic acids research. 47(D1): D427-D432.
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B (2018) The reactome pathway knowledgebase. Nucleic acids research. 46(D1): D649-D655.
Fatemi F, Hashemi-Petroudi SH, Nematzadeh G, Askari H, Abdollahi MR (2019) Exploiting differential gene expression to discover ionic and osmotic-associated transcripts in the halophyte grass Aeluropus littoralis. Biological procedures online. 21(1): 1-16.
Gao W, Xu F-C, Guo D-D, Zhao J-R, Liu J, Guo Y-W, Singh PK, Ma X-N, Long L, Botella JR (2018) Calcium-dependent protein kinases in cotton: insights into early plant responses to salt stress. BMC plant biology. 18(1): 1-15.
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM. (ed) The proteomics protocols handbook, Humana Press, New York City, New York, United States, pp571-607.
Hall T, Biosciences I, Carlsbad C (2011) BioEdit: an important software for molecular biology. GERF Bull Biosci. 2(1): 60-61.
Hamel L-P, Sheen J, Séguin A (2014) Ancient signals: comparative genomics of green plant CDPKs. Trends in plant science. 19(2): 79-89.
Harper JF, Breton G, Harmon A (2004) Decoding Ca2+ signals through plant protein kinases. Annu. Rev. Plant Biol. 55: 263-288.
Hashemi S, Nematzadeh G, Mohammadi S, Kuhlmann M (2020a) Expression pattern analysis of heat shock transcription factors (HSFs) gene family in Aeluropus littoralis under salinity stress. Environmental Stresses in Crop Sciences. 13(2).
Hashemi SH, Arab M, Dolatabadi B, Kuo Y-T, Baez MA, Himmelbach A, Nematzadeh G, Maibody SaMM, Schmutzer T, Mälzer M (2020b) Initial Description of the Genome of Aeluropus Littoralis, a Halophile Grass.
Hashemi SH, Ghorbani H (2020c) RT-qPCR analysis of some members of DEVIL gene family in Aeluropus littoralis (Gouan) Parl. under salinity stress. Environmental Stresses in Crop Sciences. 13(4): 1245-1258.
Hashemi SH, Ghorbani H, Kuhlmann M (2018) Isolation Phosphoglycerate Dehydrogenase gene from Aeluropus littoralis halophyte plant and functional analysis of T-DNA mutant in Arabidopsis thaliana. Crop Biotechnology. 8(23): 79-92.
Hashemi SH, Mohammadi S (2020d) Identification of the ERF gene family in Aeluropus littoralis halophyte plant and analysis of their expression pattern in response to salt stress. Crop Biotechnology. 9(29): 53-66.
Hashemi SH, Nematzadeh G, Askari H, Ghahary S (2014) Involvement of Cytosine DNA methylation in different developmental stages of Aeluropus littoralis. Journal of Plant Molecular Breeding. 2(2): 56-67.
Hashemi SH, Nematzadeh G, Askari H, Ghasemi Y (2012) Pattern of DNA cytosine methylation in Aeluropus littoralis during temperature stress. Journal of Plant Molecular Breeding. 1(1): 16-24.
Hashemi SH, Nematzadeh G, Kuhlmann M (2019) Identification and analysis of a DEVIL paralog gene cluster in Aeluropus littoralis by a comparative genomic approach. Crop Biotechnology. 9(25): 75-87.
Heidari P, Ahmadizadeh M, Izanlo F, Nussbaumer T (2019) In silico study of the CESA and CSL gene family in Arabidopsis thaliana and Oryza sativa: Focus on post-translation modifications. Plant Gene. 19: 100189.
Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier C, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35: 585-587.
Hrabak EM, Chan CW, Gribskov M, Harper JF, Choi JH, Halford N, Kudla J, Luan S, Nimmo HG, Sussman MR (2003) The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant physiology. 132(2): 666-680.
Jalili MM, Haddad MA, Housaindokht MR (2019) Biocomputational Investigations of Structural and Functional Properties of Cry Proteins for Malaria Biocontrol.
Jones P, Binns D, Chang H-Y, Fraser M, Li W, Mcanulla C, Mcwilliam H, Maslen J, Mitchell A, Nuka G (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics. 30(9): 1236-1240.
Kaur A, Pati PK, Pati AM, Nagpal AK (2017) In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PloS one. 12(9): e0184523.
Kaur G, Pati PK (2016) Analysis of cis-acting regulatory elements of respiratory burst oxidase homolog (Rboh) gene families in Arabidopsis and rice provides clues for their diverse functions. Computational biology and chemistry. 62: 104-118.
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D’angelo C, Bornberg‐Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV‐B light, drought and cold stress responses. The Plant Journal. 50(2): 347-363.
Kong X, Lv W, Jiang S, Zhang D, Cai G, Pan J, Li D (2013) Genome-wide identification and expression analysis of calcium-dependent protein kinase in maize. BMC genomics. 14(1): 1-15.
Ladan Moghdam A (2020) Genome wide bioinformatics analysis BES1 gene family in Vitis vinifera L. Crop Biotechnology. 10(30): 71-86.
Letunic I, Bork P (2018) 20 years of the SMART protein domain annotation resource. Nucleic acids research. 46(D1): D493-D496.
Li A-L, Zhu Y-F, Tan X-M, Wang X, Wei B, Guo H-Z, Zhang Z-L, Chen X-B, Zhao G-Y, Kong X-Y (2008) Evolutionary and functional study of the CDPK gene family in wheat (Triticum aestivum L.). Plant molecular biology. 66(4): 429-443.
Liu H, Che Z, Zeng X, Zhou X, Sitoe HM, Wang H, Yu D (2016) Genome-wide analysis of calcium-dependent protein kinases and their expression patterns in response to herbivore and wounding stresses in soybean. Functional & integrative genomics. 16(5): 481-493.
Ma S-Y, Wu W-H (2007) AtCPK23 functions in Arabidopsis responses to drought and salt stresses. Plant molecular biology. 65(4): 511-518.
Mehlmer N, Wurzinger B, Stael S, Hofmann‐Rodrigues D, Csaszar E, Pfister B, Bayer R, Teige M (2010) The Ca2+‐dependent protein kinase CPK3 is required for MAPK‐independent salt‐stress acclimation in Arabidopsis. The Plant Journal. 63(3): 484-498.
Mohammadian N (2020) Analysis of the sucrose synthase (SUS) gene family in wheat (Triticum aestivum L.) based on bioinformatics methods. Crop Biotechnology. 9(28): 37-52.
Mohanta TK, Kumar P, Bae H (2017) Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants. BMC plant biology. 17(1): 38.
Na JK, Metzger JD (2017) Guard-cell-specific expression of Arabidopsis ABF4 improves drought tolerance of tomato and tobacco. Molecular breeding. 37(12): 1-11.
Podell S, Gribskov M (2004) Predicting N-terminal myristoylation sites in plant proteins. BMC genomics. 5(1): 37.
Rezaee S, Ahmadizadeh M, Heidari P (2020) Genome-wide characterization, expression profiling, and post-transcriptional study of GASA gene family. Gene Reports. 20: 100795.
Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K (2000) Over‐expression of a single Ca2+‐dependent protein kinase confers both cold and salt/drought tolerance on rice plants. The Plant Journal. 23(3): 319-327.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nature genetics. 37(5): 501-506.
Schulz P, Herde M, Romeis T (2013) Calcium-dependent protein kinases: hubs in plant stress signaling and development. Plant physiology. 163(2): 523-530.
Sigrist CJ, De Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I (2012) New and continuing developments at PROSITE. Nucleic Acids Res. 41(D1): D344-D347.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution. 30(12): 2725-2729.
Tian W, Wang C, Gao Q, Li L, Luan S (2020) Calcium spikes, waves and oscillations in plant development and biotic interactions. Nature plants. 6(7): 750-759.
Wan B, Lin Y, Mou T (2007) Expression of rice Ca2+-dependent protein kinases (CDPKs) genes under different environmental stresses. FEBS letters. 581(6): 1179-1189.
Wang D, Liu Y-X, Yu Q, Zhao S-P, Zhao J-Y, Ru J-N, Cao X-Y, Fang Z-W, Chen J, Zhou Y-B (2019) Functional analysis of the soybean GmCDPK3 gene responding to drought and salt stresses. International journal of molecular sciences. 20(23): 5909.
Wang J-P, Xu Y-P, Munyampundu J-P, Liu T-Y, Cai X-Z (2016) Calcium-dependent protein kinase (CDPK) and CDPK-related kinase (CRK) gene families in tomato: genome-wide identification and functional analyses in disease resistance. Molecular Genetics and Genomics. 291(2): 661-676.
Wei C, Zhang R, Yang X, Zhu C, Li H, Zhang Y, Ma J, Yang J, Zhang X (2019) Comparative analysis of calcium-dependent protein kinase in Cucurbitaceae and expression studies in watermelon. International journal of molecular sciences. 20(10): 2527.
Wen F, Ye F, Xiao Z, Liao L, Li T, Jia M, Liu X, Wu X (2020) Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon. BMC genomics. 21(1):1-17.
Wernimont AK, Amani M, Qiu W, Pizarro JC, Artz JD, Lin YH, Lew J, Hutchinson A, Hui R (2011) Structures of parasitic CDPK domains point to a common mechanism of activation. Proteins: Structure, Function, and Bioinformatics. 79(3): 803-820.
Xu J, Tian Y-S, Peng R-H, Xiong A-S, Zhu B, Jin X-F, Gao F, Fu X-Y, Hou X-L, Yao Q-H (2010) AtCPK6, a functionally redundant and positive regulator involved in salt/drought stress tolerance in Arabidopsis. Planta. 231(6): 1251-1260.
Yu T-F, Zhao W-Y, Fu J-D, Liu Y-W, Chen M, Zhou Y-B, Ma Y-Z, Xu Z-S, Xi Y-J (2018) Genome-wide analysis of CDPK family in foxtail millet and determination of SiCDPK24 functions in drought stress. Frontiers in plant science. 9: 651.
Zhang H, Wei C, Yang X, Chen H, Yang Y, Mo Y, Li H, Zhang Y, Ma J, Yang J (2017a) Genome-wide identification and expression analysis of calcium‑dependent protein kinase and its related kinase gene families in melon (Cucumis melo L.). PLoS One. 12(4): e0176352.
Zhang K, Han Y-T, Zhao F-L, Hu Y, Gao Y-R, Ma Y-F, Zheng Y, Wang Y-J, Wen Y-Q (2015) Genome-wide identification and expression analysis of the CDPK gene family in grape, Vitis spp. BMC plant biology. 15(1): 1-19.
Zhang M, Liu Y, He Q, Chai M, Huang Y, Chen F, Wang X, Liu Y, Cai H, Qin Y (2020) Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress. BMC genomics. 21(1): 1-16.
Zhang M, Shen Z, Meng G, Lu Y, Wang Y (2017b) Genome-wide analysis of the Brachypodium distachyon (L.) P. Beauv. Hsp90 gene family reveals molecular evolution and expression profiling under drought and salt stresses. PloS one. 12(12): e0189187.
Zhao P, Liu Y, Kong W, Ji J, Cai T, Guo Z (2021) Genome-Wide Identification and Characterization of Calcium-Dependent Protein Kinase (CDPK) and CDPK-Related Kinase (CRK) Gene Families in Medicago truncatula. International journal of molecular sciences 22(3): 1044.

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