Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach
Tóm tắt
MicroRNAs (miRNAs) are small endogenous RNAs with an approximate length of 18–22 nucleotides and involved in the regulation of gene expression in transcriptional or post-transcriptional levels. They were found to be associated with leaf morphogenesis, flowering time, vegetative phase change, and response to environmental cues in plants, where they act as a critical regulatory factor. The nature of high conservancy of plant miRNAs within the plant species made it possible to detect the conserved miRNAs by computational approaches. Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available. To identify the novel miRNAs, a total of 46,865 ESTs from Jatropha curcas were searched for homology to all available 6746 mature miRNAs of plant eudicotyledons. Finally, we ended up with 12 novel miRNAs in Jatropha that range from 18 to 19 nucleotides where their respective precursor miRNAs had 54.11–71.76% (A + U) content. The putative miRNAs belong to 12 individual miRNA family and most of them have higher (A + U) content ranging from 47.36 to 77.77% than their respective miRNA homologs. Many of the target genes by the newly identified miRNAs were associated with plant growth and development, stress response, defense and hormone signaling, and oil synthesis pathways. These findings have the potential to speed up miRNA identification and expand our understanding of miRNA functions in J. curcas.
Tài liệu tham khảo
Openshaw K (2000) A review of Jatropha curcas: an oil plant of unfulfilled promise. Biomass Bioenergy 19(1):1–15
Singh YN, Ikahihifo T, Panuve M, Slatter C (1984) Folk medicine in Tonga. A study on the use of herbal medicines for obstetric and gynaecological conditions and disorders. J Ethnopharmacol 12(3):305–329
Staubmann Schubert-Zsilavecz M, Hiermann A, Kartnig T (1999) A complex of 5-hydroxypyrrolidin-2-one and pyrimidine-2, 4-dione isolated from Jatropha curcas. Phytochemistry 50(2):337–338
Igbinosa OO, Igbinosa EO, Aiyegoro OA (2009) Antimicrobial activity and phytochemical screening of stem bark extracts from Jatropha curcas (Linn). Afr J Pharm Pharmacol 3(2):058–062
Becker K, Makkar HP (1998) Effects of phorbol esters in carp (Cyprinus Carpio L). Vet Hum Toxicol 40(2):82–86
King AJ, He W, Cuevas JA, Freudenberger M, Ramiaramanana D, Graham IA (2009) Potential of Jatropha curcas as a source of renewable oil and animal feed. J Exp Bot 60(10):2897–2905
Achten WM, Verchot L, Franken YJ, Mathijs E, Singh VP, Aerts R, Muys B (2008) Jatropha bio-diesel production and use. Biomass Bioenergy 32(12):1063–1084
Pandey VC, Singh K, Singh JS, Kumar A, Singh B, Singh RP (2012) Jatropha curcas: a potential biofuel plant for sustainable environmental development. Renewable Sustain Energy Rev 16(5):2870–2883
Tiwari AK, Kumar A, Raheman H (2007) Biodiesel production from jatropha oil (Jatropha curcas) with high free fatty acids: an optimized process. Biomass Bioenergy 31(8):569–575
Rahman KM, Mashud M, Roknuzzaman M, Al Galib A (2010) Biodiesel from Jatropha oil as an alternative fuel for diesel engine. Int J Mech Mechatron (IJMME-IJENS) 10(3):1–6
Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46(2):243–259
Zamore PD, Haley B (2005) Ribo-gnome: the big world of small RNAs. Science 309(5740):1519–1524
Zhang B, Wang Q, Pan X (2007) MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210(2):279–289
Hawkins PG, Morris KV (2008) RNA and transcriptional modulation of gene expression. Cell Cycle 7(5):602–607
Tan Y, Zhang B, Wu T, Skogerbø G, Zhu X, Guo X, He S, Chen R (2009) Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC Mol Biol 10(1):12
Morozova N, Zinovyev A, Nonne N, Pritchard LL, Gorban AN, Harel-Bellan A (2012) Kinetic signatures of microRNA modes of action. RNA 18(9):1635–1655
Ambros V, Chen X (2007) The regulation of genes and genomes by small RNAs. Development 134(9):1635–1641
Chen X (2005) MicroRNA biogenesis and function in plants. FEBS Lett 579(26):5923–5931
Körbes AP, Machado RD, Guzman F, Almerão MP, de Oliveira LF, Loss-Morais G, Turchetto-Zolet AC, Cagliari A, dos Santos MF, Margis-Pinheiro M, Margis R (2012) Identifying conserved and novel microRNAs in developing seeds of Brassica napus using deep sequencing. PLoS ONE 7(11):e50663
Zhang B, Pan X, Cobb GP, Anderson TA (2006) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289(1):3–16
Ahmed M, Ahmed F, Ahmed J, Akhand MRN, Azim KF, Imran MAS, Hoque SF, Hasan M (2021) In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis. Heliyon 7(4):06705
Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Res 47(D1):D155–D162
Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ (2007) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:154–158
Qiu CX, Xie FL, Zhu YY, Guo K, Huang SQ, Nie L, Yang ZM (2007) Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 395(1–2):49–61
Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15:336–360
Vishwakarma NP, Jadeja VJ (2013) Identification of miRNA encoded by Jatropha curcas from EST and GSS. Plant Signaling Behav 8(2):23152
Frazier TP, Sun G, Burklew CE, Zhang B (2011) Salt and drought stresses induce the aberrant expression of microRNA genes in tobacco. Mol Biotechnol 49(2):159–165
Zhang BH, Pan X, Stellwag EJ (2008) Identification of soybean microRNAs and their targets. Planta 229:161–182
Kwak PB, Wang QQ, Chen XS, Qiu CX, Yang ZM (2009) Enrichment of a set of microRNAs during the cotton fiber development. BMC Genomics 10(1):1–11
Akter A, Islam MM, Mondal SI, Mahmud Z, Jewel NA, Ferdous S, Amin MR, Rahman MM (2014) Computational identification of miRNA and targets from expressed sequence tags of coffee (Coffea arabica). Saudi J Biol Sci 21(1):3–12
Vivek AT (2018) In silico identification and characterization of microRNAs based on EST and GSS in orphan legume crop, Lens culinaris medik(lentil). Agri Gene 8:45–56
Wang CM, Liu P, Sun F, Li L, Liu P, Ye J, Yue GH (2012) Isolation and Identification of miRNAs in Jatropha curcas. Int J Biol Sci 8(3):418–429
Galli V, Guzman F, de Oliveira LFV, Loss-Morais G, Körbes AP, Silva SDA, Margis-Pinheiro MMAN, Margis R (2014) Identifying microRNAs and transcript targets in Jatropha seeds. PLoS ONE 9(2):83727
Yang M, Lu H, Xue F, Ma L (2019) Identifying high confidence microRNAs in the developing seeds of Jatropha curcas. Sci Rep 9(1):1–11
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X (2003) A uniform system for microRNA annotation. RNA 9(3):277–279
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:140–141
Dai X, Zhao PX (2011) PsRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:155–159
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38:W214–W220
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549
Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. PNAS 95(25):14863–14868
Sunkar R, Jagadeeswaran G (2008) In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 8(37):1–13
Prabu GR, Mandal AKA (2010) Computational identification of miRNAs and their target genes from expressed sequence tags of tea (Camellia sinensis). Genomics Proteomics Bioinformatics 8(2):113–121
Bonnet E, Wuyts J, Rouze P, de Peer YV (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20(17):2911–2917
Panda D, Dehury B, Sahu J, Barooah M, Sen P, Modi MK (2014) Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene 537(2):333–342
Subburaj S, Kim AY, Lee S, Kim KN, Suh MC, Kim GJ, Lee GJ (2016) Identification of novel stress-induced microRNAs and their targets in Camelina sativa. Plant Biotechnol Rep 10(3):155–169
Felice KM, Salzman DW, Shubert-Coleman J, Jensen KP, Furneaux HM (2009) The 5′ terminal uracil of let-7a is critical for the recruitment of mRNA to Argonaute2. Biochem J 422(2):329–341
Pani A, Mahapatra RK (2013) Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags. Genom Data 1:2–6
Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Devolopmental Cell 8(4):517–527
Wang XJ, Reyes JL, Chua NH, Gaasterland T (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 5(9):1–15
Jones-Rhoades WM, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799
Axtell MJ, Bartel DP (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17(6):1658–1673
Yu F, Shi J, Zhou J, Gu J, Chen Q, Li J, Cheng W, Mao D, Tian L, Buchanan BB, Li L, Chen L, Li D, Luan S (2010) ANK6, a mitochondrial ankyrin repeat protein, is required for male-female gamete recognition in Arabidopsis thaliana. PNAS 107(51):22332–22337
Hou X, Zhou J, Liu C, Liu L, Shen L, Yu H (2014) Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nat Commun 5(1):1–14
Mukhtar MS, Deslandes L, Auriac MC, Marco Y, Somssich IE (2008) The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum. Plant J 56(6):935–947
Peng J, Yu D, Wang L, Xie M, Yuan C, Wang Y, Liu X (2012) Arabidopsis F-box gene FOA1 involved in ABA signaling. Sci China Life Sci 55(6):497–506
Higuchi M, Pischke M, Mähönen AP, Miyawaki K, Seki HY, M, Kakimoto T, (2004) In planta functions of the Arabidopsis cytokinin receptor family. PNAS 101(23):8821–8826
Mähönen AP, Higuchi M, Törmäkangas K, Miyawaki K, Pischke MS, Sussman MR, Kakimoto T (2006) Cytokinins regulate a bidirectional phosphorelay network in Arabidopsis. Curr Biol 16(11):1116–1122
Nishimura C, Ohashi Y, Sato S, Kato T, Tabata S, Ueguchi C (2004) Histidine kinase homologs that act as cytokinin receptors possess overlapping functions in the regulation of shoot and root growth in Arabidopsis. Plant Cell 16(6):1365–1377
Vogel JP, Woeste KE, Theologis A, Kieber JJ (1998) Recessive and dominant mutations in the ethylene biosynthetic gene ACS5 of Arabidopsis confer cytokinin insensitivity and ethylene overproduction, respectively. PNAS 95(8):4766–4771
Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Saito K (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. PNAS 104(15):6478–6483
Nakajima S, Sugiyama M, Iwai S, Hitomi K, Otoshi E, Kim ST, Yamamoto K (1998) Cloning and characterization of a gene (UVR3) required for photorepair of 6–4 photoproducts in Arabidopsis thaliana. Nucleic Acids Res 26(2):638–644
Ortega-Galisteo AP, Morales-Ruiz T, Ariza RR, Roldán-Arjona T (2008) Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol Biol 67(6):671–681
Schleicher E, Hitomi K, Kay CW, Getzoff ED, Todo T, Weber S (2007) Electron nuclear double resonance differentiates complementary roles for active site histidines in (6–4) photolyase. J Biol Chem 282(7):4738–4747
Gaudet P, Livstone MS, Lewis SE, Thomas PD (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform 12(5):449–462
Leung KC, Li HY, Xiao S, Tse MH, Chye ML (2006) Arabidopsis ACBP3 is an extracellularly targeted acyl-CoA-binding protein. Planta 223(5):871–881
Fan L, Zheng S, Wang X (1997) Antisense suppression of phospholipase D alpha retards abscisic acid-and ethylene-promoted senescence of postharvest Arabidopsis leaves. Plant Cell 9(12):2183–2196
Chen YQ, Kuo MS, Li S, Bui HH, Peake DA, Sanders PE, Cao G (2008) AGPAT6 is a novel microsomal glycerol-3-phosphate acyltransferase. J Biol Chem 283(15):10048–10057
Airenne TT, Kidron H, Nymalm Y, Nylund M, West G, Mattjus P, Salminen TA (2006) Structural evidence for adaptive ligand binding of glycolipid transfer protein. J Mol Biol 355(2):224–236
Nakamura Y, Koizumi R, Shui G, Shimojima M, Wenk MR, Ito T, Ohta H (2009) Arabidopsis lipins mediate eukaryotic pathway of lipid metabolism and cope critically with phosphate starvation. PNAS 106(49):20978–20983
Iida K, Fukami-Kobayashi K, Toyoda A, Sakaki Y, Kobayashi M, Seki M, Shinozaki K (2009) Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs. DNA Res 16(3):155–164